Starting phenix.real_space_refine on Wed Sep 17 03:15:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw8_39625/09_2025/8yw8_39625.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw8_39625/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yw8_39625/09_2025/8yw8_39625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw8_39625/09_2025/8yw8_39625.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yw8_39625/09_2025/8yw8_39625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw8_39625/09_2025/8yw8_39625.map" } 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-2.0-5805/lib/python3.9/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: 0.91, per 1000 atoms: 0.34 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: 0.38 Conformation dependent library (CDL) restraints added in 87.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.10 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: 0.44 Time building geometry restraints manager: 0.34 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: 2.230 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.640 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.200 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 covalent geometry : bond 0.01251 ( 2766) covalent geometry : angle 1.09627 ( 3727) SS BOND : bond 0.00692 ( 1) SS BOND : angle 4.47821 ( 2) hydrogen bonds : bond 0.16249 ( 173) hydrogen bonds : angle 6.71294 ( 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 : 0.114 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0705 time to fit residues: 2.1963 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 : 0.077 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4368 r_free = 0.4368 target = 0.222331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.148044 restraints weight = 2614.942| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.09 r_work: 0.3391 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2767 Z= 0.138 Angle : 0.484 4.917 3729 Z= 0.248 Chirality : 0.040 0.129 387 Planarity : 0.004 0.022 458 Dihedral : 15.702 71.345 455 Min Nonbonded Distance : 2.360 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 aren not related in a simple way. whole: 2.86 (0.48), residues: 323 helix: 2.48 (0.40), residues: 171 sheet: 0.24 (0.60), residues: 59 loop : 2.19 (0.72), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 7 TYR 0.009 0.001 TYR B 13 PHE 0.009 0.002 PHE B 42 TRP 0.006 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 2766) covalent geometry : angle 0.48378 ( 3727) SS BOND : bond 0.00279 ( 1) SS BOND : angle 0.43230 ( 2) hydrogen bonds : bond 0.03877 ( 173) hydrogen bonds : angle 4.25470 ( 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: 1 poor density : 21 time to evaluate : 0.084 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.0382 time to fit residues: 1.1551 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 : 0.080 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.221196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143244 restraints weight = 2698.869| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.30 r_work: 0.3368 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2767 Z= 0.119 Angle : 0.438 4.974 3729 Z= 0.224 Chirality : 0.039 0.130 387 Planarity : 0.003 0.023 458 Dihedral : 15.460 71.949 455 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.50 % Allowed : 2.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.47), residues: 323 helix: 2.67 (0.39), residues: 171 sheet: 0.25 (0.58), residues: 59 loop : 2.22 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 76 TYR 0.007 0.001 TYR B 13 PHE 0.012 0.001 PHE A 66 TRP 0.007 0.001 TRP B 44 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 2766) covalent geometry : angle 0.43801 ( 3727) SS BOND : bond 0.00242 ( 1) SS BOND : angle 0.26726 ( 2) hydrogen bonds : bond 0.03591 ( 173) hydrogen bonds : angle 4.06449 ( 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 23 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.099 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 22 average time/residue: 0.0384 time to fit residues: 1.2381 Evaluate side-chains 22 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain A residue 24 SER 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: 0.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.223500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.146376 restraints weight = 2666.186| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.24 r_work: 0.3408 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2767 Z= 0.119 Angle : 0.437 4.952 3729 Z= 0.223 Chirality : 0.039 0.130 387 Planarity : 0.003 0.023 458 Dihedral : 15.474 71.953 455 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.50 % Allowed : 2.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.47), residues: 323 helix: 2.67 (0.39), residues: 171 sheet: 0.25 (0.58), residues: 59 loop : 2.22 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 76 TYR 0.007 0.001 TYR A 62 PHE 0.012 0.001 PHE A 66 TRP 0.007 0.001 TRP B 44 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 2766) covalent geometry : angle 0.43721 ( 3727) SS BOND : bond 0.00240 ( 1) SS BOND : angle 0.26492 ( 2) hydrogen bonds : bond 0.03592 ( 173) hydrogen bonds : angle 4.06434 ( 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 22 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.099 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 21 average time/residue: 0.0373 time to fit residues: 1.1702 Evaluate side-chains 22 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain A residue 24 SER 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: 1.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.220844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143336 restraints weight = 2648.045| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.23 r_work: 0.3380 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2767 Z= 0.138 Angle : 0.435 5.030 3729 Z= 0.222 Chirality : 0.039 0.129 387 Planarity : 0.003 0.022 458 Dihedral : 15.340 72.626 455 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.50 % Allowed : 2.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.47), residues: 323 helix: 2.65 (0.39), residues: 171 sheet: 0.24 (0.58), residues: 59 loop : 2.23 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 76 TYR 0.009 0.001 TYR A 62 PHE 0.010 0.001 PHE A 66 TRP 0.005 0.001 TRP B 44 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2766) covalent geometry : angle 0.43531 ( 3727) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.16507 ( 2) hydrogen bonds : bond 0.03587 ( 173) hydrogen bonds : angle 4.02356 ( 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 23 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: B 21 GLU cc_start: 0.7344 (tt0) cc_final: 0.6541 (tt0) outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 0.0386 time to fit residues: 1.2804 Evaluate side-chains 22 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain A residue 24 SER 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: 5.9990 chunk 15 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.220824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143351 restraints weight = 2629.855| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.23 r_work: 0.3403 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2767 Z= 0.138 Angle : 0.435 5.016 3729 Z= 0.222 Chirality : 0.039 0.129 387 Planarity : 0.003 0.022 458 Dihedral : 15.340 72.626 455 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.13 % Allowed : 3.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.47), residues: 323 helix: 2.65 (0.39), residues: 171 sheet: 0.24 (0.58), residues: 59 loop : 2.23 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 76 TYR 0.009 0.001 TYR A 62 PHE 0.010 0.001 PHE A 66 TRP 0.005 0.001 TRP B 44 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2766) covalent geometry : angle 0.43512 ( 3727) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.16498 ( 2) hydrogen bonds : bond 0.03587 ( 173) hydrogen bonds : angle 4.02358 ( 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 22 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: B 21 GLU cc_start: 0.7348 (tt0) cc_final: 0.6547 (tt0) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.0348 time to fit residues: 1.1374 Evaluate side-chains 22 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain A residue 24 SER 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: 0.7980 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.220827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143351 restraints weight = 2633.731| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.23 r_work: 0.3403 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2767 Z= 0.138 Angle : 0.435 5.016 3729 Z= 0.222 Chirality : 0.039 0.129 387 Planarity : 0.003 0.022 458 Dihedral : 15.340 72.626 455 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.13 % Allowed : 3.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.47), residues: 323 helix: 2.65 (0.39), residues: 171 sheet: 0.24 (0.58), residues: 59 loop : 2.23 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 76 TYR 0.009 0.001 TYR A 62 PHE 0.010 0.001 PHE A 66 TRP 0.005 0.001 TRP B 44 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2766) covalent geometry : angle 0.43512 ( 3727) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.16498 ( 2) hydrogen bonds : bond 0.03587 ( 173) hydrogen bonds : angle 4.02358 ( 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 22 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: B 21 GLU cc_start: 0.7348 (tt0) cc_final: 0.6547 (tt0) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.0404 time to fit residues: 1.2819 Evaluate side-chains 22 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain A residue 24 SER 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: 0.0370 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 0.0470 chunk 8 optimal weight: 0.5980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.220827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143187 restraints weight = 2689.466| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.25 r_work: 0.3360 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2767 Z= 0.138 Angle : 0.435 5.016 3729 Z= 0.222 Chirality : 0.039 0.129 387 Planarity : 0.003 0.022 458 Dihedral : 15.340 72.626 455 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.50 % Allowed : 2.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.47), residues: 323 helix: 2.65 (0.39), residues: 171 sheet: 0.24 (0.58), residues: 59 loop : 2.23 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 76 TYR 0.009 0.001 TYR A 62 PHE 0.010 0.001 PHE A 66 TRP 0.005 0.001 TRP B 44 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2766) covalent geometry : angle 0.43511 ( 3727) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.16498 ( 2) hydrogen bonds : bond 0.03587 ( 173) hydrogen bonds : angle 4.02359 ( 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 23 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: B 21 GLU cc_start: 0.7339 (tt0) cc_final: 0.6541 (tt0) outliers start: 4 outliers final: 4 residues processed: 22 average time/residue: 0.0395 time to fit residues: 1.2702 Evaluate side-chains 23 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain A residue 24 SER 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: 0.0370 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.220827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143145 restraints weight = 2711.191| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.26 r_work: 0.3361 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2767 Z= 0.138 Angle : 0.435 5.016 3729 Z= 0.222 Chirality : 0.039 0.129 387 Planarity : 0.003 0.022 458 Dihedral : 15.340 72.626 455 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.50 % Allowed : 2.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.47), residues: 323 helix: 2.65 (0.39), residues: 171 sheet: 0.24 (0.58), residues: 59 loop : 2.23 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 76 TYR 0.009 0.001 TYR A 62 PHE 0.010 0.001 PHE A 66 TRP 0.005 0.001 TRP B 44 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2766) covalent geometry : angle 0.43511 ( 3727) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.16498 ( 2) hydrogen bonds : bond 0.03587 ( 173) hydrogen bonds : angle 4.02359 ( 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 23 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: B 21 GLU cc_start: 0.7338 (tt0) cc_final: 0.6543 (tt0) outliers start: 4 outliers final: 4 residues processed: 22 average time/residue: 0.0418 time to fit residues: 1.3333 Evaluate side-chains 23 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain A residue 24 SER 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: 6.9990 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.220827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143211 restraints weight = 2682.501| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.25 r_work: 0.3360 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2767 Z= 0.138 Angle : 0.435 5.016 3729 Z= 0.222 Chirality : 0.039 0.129 387 Planarity : 0.003 0.022 458 Dihedral : 15.340 72.626 455 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.50 % Allowed : 2.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.47), residues: 323 helix: 2.65 (0.39), residues: 171 sheet: 0.24 (0.58), residues: 59 loop : 2.23 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 76 TYR 0.009 0.001 TYR A 62 PHE 0.010 0.001 PHE A 66 TRP 0.005 0.001 TRP B 44 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2766) covalent geometry : angle 0.43511 ( 3727) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.16498 ( 2) hydrogen bonds : bond 0.03587 ( 173) hydrogen bonds : angle 4.02358 ( 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 23 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: B 21 GLU cc_start: 0.7341 (tt0) cc_final: 0.6543 (tt0) outliers start: 4 outliers final: 4 residues processed: 22 average time/residue: 0.0353 time to fit residues: 1.1594 Evaluate side-chains 23 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain A residue 24 SER 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: 9.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.219054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140437 restraints weight = 2673.448| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.29 r_work: 0.3374 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 2767 Z= 0.210 Angle : 0.477 5.257 3729 Z= 0.245 Chirality : 0.042 0.128 387 Planarity : 0.004 0.025 458 Dihedral : 15.259 74.618 455 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.88 % Allowed : 2.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.47), residues: 323 helix: 2.46 (0.39), residues: 171 sheet: 0.24 (0.58), residues: 59 loop : 2.25 (0.72), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 54 TYR 0.013 0.001 TYR B 13 PHE 0.011 0.002 PHE A 66 TRP 0.005 0.001 TRP B 44 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 2766) covalent geometry : angle 0.47748 ( 3727) SS BOND : bond 0.00236 ( 1) SS BOND : angle 0.26196 ( 2) hydrogen bonds : bond 0.03753 ( 173) hydrogen bonds : angle 4.07901 ( 483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1068.29 seconds wall clock time: 19 minutes 1.30 seconds (1141.30 seconds total)