Starting phenix.real_space_refine on Tue Aug 4 12:23:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw8_39625/08_2026/8yw8_39625.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw8_39625/08_2026/8yw8_39625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yw8_39625/08_2026/8yw8_39625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw8_39625/08_2026/8yw8_39625.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw8_39625/08_2026/8yw8_39625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw8_39625/08_2026/8yw8_39625.cif" } resolution = 3.17 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= 0.015 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 17 5.16 5 C 1754 2.51 5 N 454 2.21 5 O 470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2697 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1000 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "C" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 879 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "A" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 707 Classifications: {'peptide': 89} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 84} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 89 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'I2R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.00, per 1000 atoms: 0.37 Number of scatterers: 2697 At special positions: 0 Unit cell: (80.94, 74.67, 86.07, 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 17 16.00 P 2 15.00 O 470 8.00 N 454 7.00 C 1754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 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: 0.25 Conformation dependent library (CDL) restraints added in 104.2 milliseconds 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 606 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 64.4% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 40 through 49 removed outlier: 3.643A pdb=" N TRP B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 49 through 59 removed outlier: 3.994A pdb=" N VAL B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 89 removed outlier: 3.513A pdb=" N LEU B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 126 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'A' and resid 24 through 34 Proline residue: A 30 - end of helix removed outlier: 3.868A pdb=" N TRP A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 77 through 108 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.404A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.404A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 483 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: 0.25 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 402 1.26 - 1.40: 719 1.40 - 1.53: 1473 1.53 - 1.67: 142 1.67 - 1.81: 30 Bond restraints: 2766 Sorted by residual: bond pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 1.331 1.438 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 1.339 1.444 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 1.334 1.437 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C19 I2R A 201 " pdb=" C22 I2R A 201 " ideal model delta sigma weight residual 1.419 1.519 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 1.333 1.431 -0.098 2.00e-02 2.50e+03 2.38e+01 ... (remaining 2761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 3582 2.59 - 5.18: 122 5.18 - 7.76: 13 7.76 - 10.35: 6 10.35 - 12.94: 4 Bond angle restraints: 3727 Sorted by residual: angle pdb=" N ASP C 52 " pdb=" CA ASP C 52 " pdb=" C ASP C 52 " ideal model delta sigma weight residual 109.79 118.15 -8.36 1.56e+00 4.11e-01 2.87e+01 angle pdb=" OB3 CDL B 201 " pdb=" PB2 CDL B 201 " pdb=" OB4 CDL B 201 " ideal model delta sigma weight residual 121.80 108.86 12.94 3.00e+00 1.11e-01 1.86e+01 angle pdb=" OA2 CDL B 201 " pdb=" PA1 CDL B 201 " pdb=" OA5 CDL B 201 " ideal model delta sigma weight residual 97.81 110.63 -12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" OA3 CDL B 201 " pdb=" PA1 CDL B 201 " pdb=" OA4 CDL B 201 " ideal model delta sigma weight residual 121.92 109.34 12.58 3.00e+00 1.11e-01 1.76e+01 angle pdb=" OB2 CDL B 201 " pdb=" PB2 CDL B 201 " pdb=" OB5 CDL B 201 " ideal model delta sigma weight residual 96.70 109.07 -12.37 3.00e+00 1.11e-01 1.70e+01 ... (remaining 3722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 1519 17.94 - 35.87: 91 35.87 - 53.81: 36 53.81 - 71.74: 21 71.74 - 89.68: 3 Dihedral angle restraints: 1670 sinusoidal: 723 harmonic: 947 Sorted by residual: dihedral pdb=" C ASP C 52 " pdb=" N ASP C 52 " pdb=" CA ASP C 52 " pdb=" CB ASP C 52 " ideal model delta harmonic sigma weight residual -122.60 -132.20 9.60 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" CA PHE A 66 " pdb=" C PHE A 66 " pdb=" N MET A 67 " pdb=" CA MET A 67 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" N ASP C 52 " pdb=" C ASP C 52 " pdb=" CA ASP C 52 " pdb=" CB ASP C 52 " ideal model delta harmonic sigma weight residual 122.80 130.72 -7.92 0 2.50e+00 1.60e-01 1.00e+01 ... (remaining 1667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 295 0.065 - 0.130: 74 0.130 - 0.194: 15 0.194 - 0.259: 2 0.259 - 0.324: 1 Chirality restraints: 387 Sorted by residual: chirality pdb=" CA ASP C 52 " pdb=" N ASP C 52 " pdb=" C ASP C 52 " pdb=" CB ASP C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA ASN B 93 " pdb=" N ASN B 93 " pdb=" C ASN B 93 " pdb=" CB ASN B 93 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA GLN C 54 " pdb=" N GLN C 54 " pdb=" C GLN C 54 " pdb=" CB GLN C 54 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 384 not shown) Planarity restraints: 458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 I2R A 201 " -0.002 2.00e-02 2.50e+03 1.22e-02 4.11e+00 pdb=" C11 I2R A 201 " -0.001 2.00e-02 2.50e+03 pdb=" C12 I2R A 201 " -0.012 2.00e-02 2.50e+03 pdb=" C13 I2R A 201 " -0.006 2.00e-02 2.50e+03 pdb=" C14 I2R A 201 " 0.001 2.00e-02 2.50e+03 pdb=" C5 I2R A 201 " 0.002 2.00e-02 2.50e+03 pdb=" C6 I2R A 201 " 0.000 2.00e-02 2.50e+03 pdb=" C7 I2R A 201 " 0.018 2.00e-02 2.50e+03 pdb=" C8 I2R A 201 " -0.012 2.00e-02 2.50e+03 pdb=" C9 I2R A 201 " -0.016 2.00e-02 2.50e+03 pdb=" N3 I2R A 201 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 I2R A 201 " 0.019 2.00e-02 2.50e+03 1.56e-02 3.03e+00 pdb=" C19 I2R A 201 " 0.016 2.00e-02 2.50e+03 pdb=" C21 I2R A 201 " -0.017 2.00e-02 2.50e+03 pdb=" C22 I2R A 201 " -0.000 2.00e-02 2.50e+03 pdb=" C7 I2R A 201 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 99 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C VAL B 99 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL B 99 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN B 100 " 0.009 2.00e-02 2.50e+03 ... (remaining 455 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 892 2.85 - 3.37: 2499 3.37 - 3.88: 4638 3.88 - 4.39: 5400 4.39 - 4.90: 8798 Nonbonded interactions: 22227 Sorted by model distance: nonbonded pdb=" OA6 CDL B 201 " pdb=" OA8 CDL B 201 " model vdw 2.342 2.432 nonbonded pdb=" O1 CDL B 201 " pdb=" OA2 CDL B 201 " model vdw 2.439 2.432 nonbonded pdb=" OD2 ASP C 73 " pdb=" NZ LYS C 76 " model vdw 2.449 3.120 nonbonded pdb=" C15 I2R A 201 " pdb=" C8 I2R A 201 " model vdw 2.484 2.848 nonbonded pdb=" O PRO B 38 " pdb=" NE1 TRP B 44 " model vdw 2.569 3.120 ... (remaining 22222 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: 1.950 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.760 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.012 0.107 2767 Z= 0.689 Angle : 1.182 12.938 3729 Z= 0.690 Chirality : 0.060 0.324 387 Planarity : 0.004 0.032 458 Dihedral : 15.881 89.676 1061 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.47), residues: 323 helix: 0.91 (0.37), residues: 171 sheet: -0.10 (0.70), residues: 55 loop : 2.14 (0.70), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 10 TYR 0.015 0.001 TYR B 85 PHE 0.001 0.000 PHE A 57 TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.01157 / 0.69 ( 2766) covalent geometry : angle 1.17763 / 0.69 ( 3727) SS BOND : bond 0.00692 / 0.36 ( 1) SS BOND : angle 4.47821 / 2.62 ( 2) hydrogen bonds : bond 0.16249 / 10.95 ( 173) hydrogen bonds : angle 6.71294 / 4.81 ( 483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.093 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0618 time to fit residues: 1.9585 Evaluate side-chains 21 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** 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 = 0.4385 r_free = 0.4385 target = 0.224363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147836 restraints weight = 2637.492| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.24 r_work: 0.3426 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2767 Z= 0.149 Angle : 0.535 5.359 3729 Z= 0.270 Chirality : 0.041 0.135 387 Planarity : 0.004 0.024 458 Dihedral : 15.523 74.221 471 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.75 % Allowed : 2.63 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.47), residues: 323 helix: 2.24 (0.39), residues: 171 sheet: 0.24 (0.59), residues: 59 loop : 2.49 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.009 0.001 TYR B 13 PHE 0.011 0.001 PHE A 66 TRP 0.008 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 2766) covalent geometry : angle 0.53538 / 0.27 ( 3727) SS BOND : bond 0.00164 / 0.09 ( 1) SS BOND : angle 0.42212 / 0.25 ( 2) hydrogen bonds : bond 0.04757 / 3.25 ( 173) hydrogen bonds : angle 4.61489 / 3.39 ( 483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.091 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.0476 time to fit residues: 1.3792 Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain A residue 47 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** 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 = 0.4388 r_free = 0.4388 target = 0.224659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147477 restraints weight = 2698.312| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.29 r_work: 0.3441 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2767 Z= 0.149 Angle : 0.535 5.359 3729 Z= 0.270 Chirality : 0.041 0.135 387 Planarity : 0.004 0.024 458 Dihedral : 15.523 74.221 471 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.75 % Allowed : 3.01 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.47), residues: 323 helix: 2.24 (0.39), residues: 171 sheet: 0.24 (0.59), residues: 59 loop : 2.49 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.009 0.001 TYR B 13 PHE 0.011 0.001 PHE A 66 TRP 0.008 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 2766) covalent geometry : angle 0.53494 / 0.27 ( 3727) SS BOND : bond 0.00164 / 0.09 ( 1) SS BOND : angle 0.42210 / 0.25 ( 2) hydrogen bonds : bond 0.04758 / 3.25 ( 173) hydrogen bonds : angle 4.61488 / 3.39 ( 483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.094 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.0383 time to fit residues: 1.0794 Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain A residue 47 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.0170 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.0570 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** 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 = 0.4388 r_free = 0.4388 target = 0.224659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147576 restraints weight = 2669.627| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.29 r_work: 0.3385 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2767 Z= 0.149 Angle : 0.535 5.359 3729 Z= 0.270 Chirality : 0.041 0.135 387 Planarity : 0.004 0.024 458 Dihedral : 15.523 74.221 471 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.75 % Allowed : 3.01 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.47), residues: 323 helix: 2.24 (0.39), residues: 171 sheet: 0.24 (0.59), residues: 59 loop : 2.49 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.009 0.001 TYR B 13 PHE 0.011 0.001 PHE A 66 TRP 0.008 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 2766) covalent geometry : angle 0.53494 / 0.27 ( 3727) SS BOND : bond 0.00164 / 0.09 ( 1) SS BOND : angle 0.42210 / 0.25 ( 2) hydrogen bonds : bond 0.04758 / 3.25 ( 173) hydrogen bonds : angle 4.61488 / 3.39 ( 483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.057 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.0237 time to fit residues: 0.6706 Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain A residue 47 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** 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 = 0.4388 r_free = 0.4388 target = 0.224659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147610 restraints weight = 2658.935| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.28 r_work: 0.3387 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2767 Z= 0.149 Angle : 0.535 5.359 3729 Z= 0.270 Chirality : 0.041 0.135 387 Planarity : 0.004 0.024 458 Dihedral : 15.523 74.221 471 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.75 % Allowed : 3.01 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.47), residues: 323 helix: 2.24 (0.39), residues: 171 sheet: 0.24 (0.59), residues: 59 loop : 2.49 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.009 0.001 TYR B 13 PHE 0.011 0.001 PHE A 66 TRP 0.008 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 2766) covalent geometry : angle 0.53494 / 0.27 ( 3727) SS BOND : bond 0.00164 / 0.09 ( 1) SS BOND : angle 0.42210 / 0.25 ( 2) hydrogen bonds : bond 0.04758 / 3.25 ( 173) hydrogen bonds : angle 4.61488 / 3.39 ( 483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.059 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.0300 time to fit residues: 0.8521 Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain A residue 47 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** 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 = 0.4388 r_free = 0.4388 target = 0.224659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147657 restraints weight = 2638.646| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.28 r_work: 0.3386 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2767 Z= 0.149 Angle : 0.535 5.359 3729 Z= 0.270 Chirality : 0.041 0.135 387 Planarity : 0.004 0.024 458 Dihedral : 15.523 74.221 471 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.75 % Allowed : 3.01 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.47), residues: 323 helix: 2.24 (0.39), residues: 171 sheet: 0.24 (0.59), residues: 59 loop : 2.49 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.009 0.001 TYR B 13 PHE 0.011 0.001 PHE A 66 TRP 0.008 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 2766) covalent geometry : angle 0.53494 / 0.27 ( 3727) SS BOND : bond 0.00164 / 0.09 ( 1) SS BOND : angle 0.42210 / 0.25 ( 2) hydrogen bonds : bond 0.04758 / 3.25 ( 173) hydrogen bonds : angle 4.61488 / 3.39 ( 483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.118 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.0412 time to fit residues: 1.1848 Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain A residue 47 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 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 = 0.4411 r_free = 0.4411 target = 0.226211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.150026 restraints weight = 2638.092| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.24 r_work: 0.3439 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2767 Z= 0.175 Angle : 0.524 5.666 3729 Z= 0.260 Chirality : 0.041 0.132 387 Planarity : 0.004 0.027 458 Dihedral : 15.457 73.585 471 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.75 % Allowed : 3.01 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.46), residues: 323 helix: 2.26 (0.38), residues: 171 sheet: 0.27 (0.58), residues: 59 loop : 2.44 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 113 TYR 0.009 0.001 TYR B 13 PHE 0.009 0.001 PHE A 66 TRP 0.004 0.001 TRP B 94 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 2766) covalent geometry : angle 0.52441 / 0.26 ( 3727) SS BOND : bond 0.00194 / 0.10 ( 1) SS BOND : angle 0.21154 / 0.12 ( 2) hydrogen bonds : bond 0.04639 / 3.17 ( 173) hydrogen bonds : angle 4.56996 / 3.36 ( 483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.100 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.0347 time to fit residues: 0.9868 Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain A residue 47 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 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 = 0.4347 r_free = 0.4347 target = 0.221539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143672 restraints weight = 2695.908| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.30 r_work: 0.3368 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2767 Z= 0.180 Angle : 0.524 5.666 3729 Z= 0.260 Chirality : 0.041 0.132 387 Planarity : 0.004 0.022 458 Dihedral : 15.457 73.585 471 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.75 % Allowed : 3.01 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.46), residues: 323 helix: 2.26 (0.38), residues: 171 sheet: 0.27 (0.58), residues: 59 loop : 2.44 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 113 TYR 0.009 0.001 TYR B 13 PHE 0.009 0.001 PHE A 66 TRP 0.004 0.001 TRP B 94 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 2766) covalent geometry : angle 0.52405 / 0.26 ( 3727) SS BOND : bond 0.00194 / 0.10 ( 1) SS BOND : angle 0.21154 / 0.12 ( 2) hydrogen bonds : bond 0.04639 / 3.17 ( 173) hydrogen bonds : angle 4.56996 / 3.36 ( 483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.056 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.0261 time to fit residues: 0.7304 Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain A residue 47 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 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 = 0.4347 r_free = 0.4347 target = 0.221539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143628 restraints weight = 2715.965| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.30 r_work: 0.3368 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2767 Z= 0.180 Angle : 0.524 5.666 3729 Z= 0.260 Chirality : 0.041 0.132 387 Planarity : 0.004 0.022 458 Dihedral : 15.457 73.585 471 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.75 % Allowed : 3.01 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.46), residues: 323 helix: 2.26 (0.38), residues: 171 sheet: 0.27 (0.58), residues: 59 loop : 2.44 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 113 TYR 0.009 0.001 TYR B 13 PHE 0.009 0.001 PHE A 66 TRP 0.004 0.001 TRP B 94 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 2766) covalent geometry : angle 0.52405 / 0.26 ( 3727) SS BOND : bond 0.00194 / 0.10 ( 1) SS BOND : angle 0.21154 / 0.12 ( 2) hydrogen bonds : bond 0.04639 / 3.17 ( 173) hydrogen bonds : angle 4.56996 / 3.36 ( 483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.057 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.0282 time to fit residues: 0.7727 Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain A residue 47 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 28 optimal weight: 0.0980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 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 = 0.4347 r_free = 0.4347 target = 0.221539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143699 restraints weight = 2689.295| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.29 r_work: 0.3369 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2767 Z= 0.180 Angle : 0.524 5.666 3729 Z= 0.260 Chirality : 0.041 0.132 387 Planarity : 0.004 0.022 458 Dihedral : 15.458 73.585 471 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.75 % Allowed : 3.01 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.46), residues: 323 helix: 2.26 (0.38), residues: 171 sheet: 0.27 (0.58), residues: 59 loop : 2.44 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 113 TYR 0.009 0.001 TYR B 13 PHE 0.009 0.001 PHE A 66 TRP 0.004 0.001 TRP B 94 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 2766) covalent geometry : angle 0.52401 / 0.26 ( 3727) SS BOND : bond 0.00194 / 0.10 ( 1) SS BOND : angle 0.21149 / 0.12 ( 2) hydrogen bonds : bond 0.04639 / 3.17 ( 173) hydrogen bonds : angle 4.56996 / 3.36 ( 483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.066 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.0260 time to fit residues: 0.7277 Evaluate side-chains 20 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain A residue 47 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.0970 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 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 = 0.4417 r_free = 0.4417 target = 0.226898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150459 restraints weight = 2648.516| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.26 r_work: 0.3380 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2767 Z= 0.129 Angle : 0.490 5.270 3729 Z= 0.245 Chirality : 0.040 0.137 387 Planarity : 0.003 0.022 458 Dihedral : 15.364 72.397 471 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.38 % Allowed : 3.38 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.46), residues: 323 helix: 2.43 (0.39), residues: 171 sheet: 0.28 (0.58), residues: 59 loop : 2.42 (0.70), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.008 0.001 TYR B 13 PHE 0.010 0.002 PHE A 66 TRP 0.004 0.001 TRP B 94 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 2766) covalent geometry : angle 0.49028 / 0.24 ( 3727) SS BOND : bond 0.00152 / 0.08 ( 1) SS BOND : angle 0.34559 / 0.20 ( 2) hydrogen bonds : bond 0.04435 / 3.03 ( 173) hydrogen bonds : angle 4.47185 / 3.27 ( 483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 896.77 seconds wall clock time: 15 minutes 58.36 seconds (958.36 seconds total)