Starting phenix.real_space_refine on Wed Jul 23 09:05:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw8_39625/07_2025/8yw8_39625.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw8_39625/07_2025/8yw8_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_39625/07_2025/8yw8_39625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw8_39625/07_2025/8yw8_39625.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw8_39625/07_2025/8yw8_39625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw8_39625/07_2025/8yw8_39625.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 2.93, per 1000 atoms: 1.09 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: 0.80 Conformation dependent library (CDL) restraints added in 314.5 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: 0.33 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: 0.70 Time building geometry restraints manager: 0.90 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=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 1.334 1.444 -0.110 1.10e-02 8.26e+03 9.97e+01 bond pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 1.334 1.438 -0.104 1.10e-02 8.26e+03 8.86e+01 bond pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 1.342 1.437 -0.095 1.50e-02 4.44e+03 4.01e+01 bond pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 1.342 1.431 -0.089 1.50e-02 4.44e+03 3.49e+01 bond pdb=" OB2 CDL B 201 " pdb=" PB2 CDL B 201 " ideal model delta sigma weight residual 1.579 1.665 -0.086 1.50e-02 4.44e+03 3.27e+01 ... (remaining 2761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 3461 1.90 - 3.81: 227 3.81 - 5.71: 22 5.71 - 7.62: 8 7.62 - 9.52: 9 Bond angle restraints: 3727 Sorted by residual: angle pdb=" C51 CDL B 201 " pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 111.33 119.80 -8.47 1.32e+00 5.72e-01 4.11e+01 angle pdb=" C11 CDL B 201 " pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 111.33 119.78 -8.45 1.32e+00 5.72e-01 4.08e+01 angle pdb=" C31 CDL B 201 " pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 111.64 121.16 -9.52 1.65e+00 3.69e-01 3.34e+01 angle pdb=" C71 CDL B 201 " pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 111.64 120.61 -8.97 1.65e+00 3.69e-01 2.97e+01 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 ... (remaining 3722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 1496 17.94 - 35.87: 87 35.87 - 53.81: 49 53.81 - 71.74: 18 71.74 - 89.68: 4 Dihedral angle restraints: 1654 sinusoidal: 707 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 1651 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.360 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 : 0.013 0.110 2767 Z= 0.780 Angle : 1.101 9.520 3729 Z= 0.715 Chirality : 0.060 0.324 387 Planarity : 0.004 0.032 458 Dihedral : 16.721 89.676 1045 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (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 TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS A 84 PHE 0.001 0.000 PHE A 57 TYR 0.015 0.001 TYR B 85 ARG 0.001 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.16249 ( 173) hydrogen bonds : angle 6.71294 ( 483) SS BOND : bond 0.00692 ( 1) SS BOND : angle 4.47821 ( 2) covalent geometry : bond 0.01251 ( 2766) covalent geometry : angle 1.09627 ( 3727) *********************** 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 : 0.255 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1629 time to fit residues: 5.0874 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 : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 20.0000 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.0020 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4393 r_free = 0.4393 target = 0.225588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.149342 restraints weight = 2644.836| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.23 r_work: 0.3333 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2767 Z= 0.127 Angle : 0.483 5.190 3729 Z= 0.248 Chirality : 0.040 0.141 387 Planarity : 0.004 0.021 458 Dihedral : 16.482 76.189 455 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.47), residues: 323 helix: 2.48 (0.39), residues: 171 sheet: 0.19 (0.60), residues: 59 loop : 2.35 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 PHE 0.007 0.001 PHE A 66 TYR 0.009 0.001 TYR B 13 ARG 0.002 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 173) hydrogen bonds : angle 4.41733 ( 483) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.35912 ( 2) covalent geometry : bond 0.00265 ( 2766) covalent geometry : angle 0.48312 ( 3727) *********************** 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 21 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.250 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.1161 time to fit residues: 3.3078 Evaluate side-chains 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 12 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4394 r_free = 0.4394 target = 0.225732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149325 restraints weight = 2619.787| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.25 r_work: 0.3422 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2767 Z= 0.128 Angle : 0.483 5.187 3729 Z= 0.248 Chirality : 0.040 0.140 387 Planarity : 0.003 0.021 458 Dihedral : 16.484 76.189 455 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.38 % Allowed : 3.76 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.47), residues: 323 helix: 2.48 (0.39), residues: 171 sheet: 0.19 (0.60), residues: 59 loop : 2.35 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 PHE 0.007 0.001 PHE A 66 TYR 0.009 0.001 TYR B 13 ARG 0.002 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 173) hydrogen bonds : angle 4.41732 ( 483) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.35907 ( 2) covalent geometry : bond 0.00266 ( 2766) covalent geometry : angle 0.48271 ( 3727) *********************** 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 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.318 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.1313 time to fit residues: 3.5196 Evaluate side-chains 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 15 optimal weight: 0.3980 chunk 2 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.0170 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4394 r_free = 0.4394 target = 0.225744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149182 restraints weight = 2669.145| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.27 r_work: 0.3401 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2767 Z= 0.126 Angle : 0.482 5.138 3729 Z= 0.248 Chirality : 0.040 0.140 387 Planarity : 0.003 0.021 458 Dihedral : 16.495 76.185 455 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.38 % Allowed : 3.76 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.47), residues: 323 helix: 2.48 (0.39), residues: 171 sheet: 0.19 (0.60), residues: 59 loop : 2.35 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 PHE 0.007 0.001 PHE A 66 TYR 0.009 0.001 TYR B 13 ARG 0.002 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 173) hydrogen bonds : angle 4.41737 ( 483) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.35850 ( 2) covalent geometry : bond 0.00265 ( 2766) covalent geometry : angle 0.48210 ( 3727) *********************** 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 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.292 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.1206 time to fit residues: 3.3523 Evaluate side-chains 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4428 r_free = 0.4428 target = 0.228325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.152401 restraints weight = 2639.830| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.26 r_work: 0.3407 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2767 Z= 0.124 Angle : 0.480 4.997 3729 Z= 0.246 Chirality : 0.040 0.136 387 Planarity : 0.003 0.022 458 Dihedral : 16.559 76.167 455 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.38 % Allowed : 3.76 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.47), residues: 323 helix: 2.49 (0.39), residues: 171 sheet: 0.19 (0.60), residues: 59 loop : 2.35 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 PHE 0.007 0.001 PHE A 66 TYR 0.009 0.001 TYR B 13 ARG 0.002 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 173) hydrogen bonds : angle 4.41745 ( 483) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.35552 ( 2) covalent geometry : bond 0.00265 ( 2766) covalent geometry : angle 0.47966 ( 3727) *********************** 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 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.266 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.0890 time to fit residues: 2.5506 Evaluate side-chains 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.0010 chunk 14 optimal weight: 0.0670 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4393 r_free = 0.4393 target = 0.225706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.149792 restraints weight = 2640.724| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.23 r_work: 0.3450 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2767 Z= 0.118 Angle : 0.460 4.941 3729 Z= 0.232 Chirality : 0.039 0.131 387 Planarity : 0.003 0.025 458 Dihedral : 16.341 74.258 455 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.47), residues: 323 helix: 2.57 (0.39), residues: 171 sheet: 0.25 (0.59), residues: 59 loop : 2.32 (0.70), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 94 HIS 0.004 0.001 HIS A 84 PHE 0.009 0.001 PHE A 66 TYR 0.009 0.001 TYR A 62 ARG 0.001 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 173) hydrogen bonds : angle 4.33863 ( 483) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.18589 ( 2) covalent geometry : bond 0.00255 ( 2766) covalent geometry : angle 0.46057 ( 3727) *********************** 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 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.272 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.0986 time to fit residues: 2.8555 Evaluate side-chains 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4394 r_free = 0.4394 target = 0.225780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149375 restraints weight = 2714.421| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.28 r_work: 0.3403 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2767 Z= 0.119 Angle : 0.460 4.948 3729 Z= 0.232 Chirality : 0.039 0.131 387 Planarity : 0.003 0.025 458 Dihedral : 16.343 74.255 455 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.47), residues: 323 helix: 2.57 (0.39), residues: 171 sheet: 0.25 (0.59), residues: 59 loop : 2.32 (0.70), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 PHE 0.009 0.001 PHE A 66 TYR 0.009 0.001 TYR A 62 ARG 0.001 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 173) hydrogen bonds : angle 4.33840 ( 483) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.18554 ( 2) covalent geometry : bond 0.00256 ( 2766) covalent geometry : angle 0.45991 ( 3727) *********************** 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 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.241 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.1036 time to fit residues: 2.8407 Evaluate side-chains 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.0370 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4394 r_free = 0.4394 target = 0.225780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149611 restraints weight = 2623.528| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.24 r_work: 0.3427 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2767 Z= 0.119 Angle : 0.460 4.948 3729 Z= 0.232 Chirality : 0.039 0.131 387 Planarity : 0.003 0.025 458 Dihedral : 16.340 74.255 455 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.47), residues: 323 helix: 2.57 (0.39), residues: 171 sheet: 0.25 (0.59), residues: 59 loop : 2.32 (0.70), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 PHE 0.009 0.001 PHE A 66 TYR 0.009 0.001 TYR A 62 ARG 0.001 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 173) hydrogen bonds : angle 4.33840 ( 483) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.18554 ( 2) covalent geometry : bond 0.00256 ( 2766) covalent geometry : angle 0.45991 ( 3727) *********************** 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 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.295 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.0981 time to fit residues: 2.7864 Evaluate side-chains 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 20 optimal weight: 7.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4394 r_free = 0.4394 target = 0.225780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149566 restraints weight = 2637.560| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.25 r_work: 0.3406 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2767 Z= 0.119 Angle : 0.460 4.948 3729 Z= 0.232 Chirality : 0.039 0.131 387 Planarity : 0.003 0.025 458 Dihedral : 16.340 74.255 455 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.47), residues: 323 helix: 2.57 (0.39), residues: 171 sheet: 0.25 (0.59), residues: 59 loop : 2.32 (0.70), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 PHE 0.009 0.001 PHE A 66 TYR 0.009 0.001 TYR A 62 ARG 0.001 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 173) hydrogen bonds : angle 4.33840 ( 483) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.18554 ( 2) covalent geometry : bond 0.00256 ( 2766) covalent geometry : angle 0.45991 ( 3727) *********************** 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 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.399 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.1042 time to fit residues: 2.9010 Evaluate side-chains 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 22 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4394 r_free = 0.4394 target = 0.225780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149380 restraints weight = 2690.428| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.27 r_work: 0.3420 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2767 Z= 0.119 Angle : 0.460 4.948 3729 Z= 0.232 Chirality : 0.039 0.131 387 Planarity : 0.003 0.025 458 Dihedral : 16.340 74.255 455 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.47), residues: 323 helix: 2.57 (0.39), residues: 171 sheet: 0.25 (0.59), residues: 59 loop : 2.32 (0.70), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 PHE 0.009 0.001 PHE A 66 TYR 0.009 0.001 TYR A 62 ARG 0.001 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 173) hydrogen bonds : angle 4.33840 ( 483) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.18554 ( 2) covalent geometry : bond 0.00256 ( 2766) covalent geometry : angle 0.45991 ( 3727) ********************** 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 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.297 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.1023 time to fit residues: 2.8399 Evaluate side-chains 19 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 6 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4394 r_free = 0.4394 target = 0.225780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149630 restraints weight = 2616.189| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.24 r_work: 0.3428 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2767 Z= 0.119 Angle : 0.460 4.948 3729 Z= 0.232 Chirality : 0.039 0.131 387 Planarity : 0.003 0.025 458 Dihedral : 16.340 74.255 455 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.47), residues: 323 helix: 2.57 (0.39), residues: 171 sheet: 0.25 (0.59), residues: 59 loop : 2.32 (0.70), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 94 HIS 0.003 0.001 HIS A 84 PHE 0.009 0.001 PHE A 66 TYR 0.009 0.001 TYR A 62 ARG 0.001 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 173) hydrogen bonds : angle 4.33840 ( 483) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.18554 ( 2) covalent geometry : bond 0.00256 ( 2766) covalent geometry : angle 0.45991 ( 3727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2189.30 seconds wall clock time: 38 minutes 47.65 seconds (2327.65 seconds total)