Starting phenix.real_space_refine on Wed Sep 17 04:18:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rm8_19353/09_2025/8rm8_19353_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rm8_19353/09_2025/8rm8_19353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rm8_19353/09_2025/8rm8_19353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rm8_19353/09_2025/8rm8_19353.map" model { file = "/net/cci-nas-00/data/ceres_data/8rm8_19353/09_2025/8rm8_19353_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rm8_19353/09_2025/8rm8_19353_trim.cif" } resolution = 3.0 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= 0.004 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 1265 2.51 5 N 370 2.21 5 O 400 1.98 5 H 1915 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 3950 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 347 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 441 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, F, G, J, C, E, H, K Time building chain proxies: 0.76, per 1000 atoms: 0.19 Number of scatterers: 3950 At special positions: 0 Unit cell: (59.136, 61.952, 45.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 400 8.00 N 370 7.00 C 1265 6.00 H 1915 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 92.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 500 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 3 sheets defined 0.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 removed outlier: 3.849A pdb=" N VAL D 17 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL F 17 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL G 17 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL J 17 " --> pdb=" O LEU G 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 23 Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.525A pdb=" N ASN B 35 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER C 34 " --> pdb=" O ASN E 35 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN C 35 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN H 35 " --> pdb=" O SER K 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 8 hydrogen bonds defined for protein. 24 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: 0.72 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.98: 1915 0.98 - 1.12: 0 1.12 - 1.27: 325 1.27 - 1.41: 570 1.41 - 1.55: 1170 Bond restraints: 3980 Sorted by residual: bond pdb=" CB VAL E 17 " pdb=" CG1 VAL E 17 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.83e+00 bond pdb=" CB VAL B 17 " pdb=" CG1 VAL B 17 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.80e+00 bond pdb=" CB VAL C 17 " pdb=" CG1 VAL C 17 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.79e+00 bond pdb=" CB VAL H 17 " pdb=" CG1 VAL H 17 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.78e+00 bond pdb=" CB VAL K 17 " pdb=" CG1 VAL K 17 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.69e+00 ... (remaining 3975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 6757 2.52 - 5.04: 283 5.04 - 7.56: 20 7.56 - 10.08: 0 10.08 - 12.60: 5 Bond angle restraints: 7065 Sorted by residual: angle pdb=" CA PRO C 28 " pdb=" N PRO C 28 " pdb=" CD PRO C 28 " ideal model delta sigma weight residual 112.00 106.60 5.40 1.40e+00 5.10e-01 1.49e+01 angle pdb=" CA PRO B 28 " pdb=" N PRO B 28 " pdb=" CD PRO B 28 " ideal model delta sigma weight residual 112.00 106.61 5.39 1.40e+00 5.10e-01 1.48e+01 angle pdb=" CA PRO E 28 " pdb=" N PRO E 28 " pdb=" CD PRO E 28 " ideal model delta sigma weight residual 112.00 106.63 5.37 1.40e+00 5.10e-01 1.47e+01 angle pdb=" CA PRO H 28 " pdb=" N PRO H 28 " pdb=" CD PRO H 28 " ideal model delta sigma weight residual 112.00 106.64 5.36 1.40e+00 5.10e-01 1.46e+01 angle pdb=" CA PRO K 28 " pdb=" N PRO K 28 " pdb=" CD PRO K 28 " ideal model delta sigma weight residual 112.00 106.65 5.35 1.40e+00 5.10e-01 1.46e+01 ... (remaining 7060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 1655 15.87 - 31.74: 199 31.74 - 47.61: 56 47.61 - 63.48: 15 63.48 - 79.35: 20 Dihedral angle restraints: 1945 sinusoidal: 1005 harmonic: 940 Sorted by residual: dihedral pdb=" CA VAL G 17 " pdb=" C VAL G 17 " pdb=" N HIS G 18 " pdb=" CA HIS G 18 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA VAL A 17 " pdb=" C VAL A 17 " pdb=" N HIS A 18 " pdb=" CA HIS A 18 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA VAL D 17 " pdb=" C VAL D 17 " pdb=" N HIS D 18 " pdb=" CA HIS D 18 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 1942 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.052: 195 0.052 - 0.103: 110 0.103 - 0.155: 15 0.155 - 0.206: 5 0.206 - 0.257: 5 Chirality restraints: 330 Sorted by residual: chirality pdb=" CB VAL E 17 " pdb=" CA VAL E 17 " pdb=" CG1 VAL E 17 " pdb=" CG2 VAL E 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL K 17 " pdb=" CA VAL K 17 " pdb=" CG1 VAL K 17 " pdb=" CG2 VAL K 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL B 17 " pdb=" CA VAL B 17 " pdb=" CG1 VAL B 17 " pdb=" CG2 VAL B 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 327 not shown) Planarity restraints: 620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 18 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" C HIS B 18 " 0.041 2.00e-02 2.50e+03 pdb=" O HIS B 18 " -0.016 2.00e-02 2.50e+03 pdb=" N SER B 19 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS K 18 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C HIS K 18 " 0.041 2.00e-02 2.50e+03 pdb=" O HIS K 18 " -0.016 2.00e-02 2.50e+03 pdb=" N SER K 19 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 18 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C HIS H 18 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS H 18 " -0.015 2.00e-02 2.50e+03 pdb=" N SER H 19 " -0.013 2.00e-02 2.50e+03 ... (remaining 617 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.28: 727 2.28 - 2.84: 8239 2.84 - 3.39: 9491 3.39 - 3.95: 12907 3.95 - 4.50: 18539 Nonbonded interactions: 49903 Sorted by model distance: nonbonded pdb=" O GLY E 24 " pdb="HD22 ASN G 21 " model vdw 1.729 2.450 nonbonded pdb=" O GLY B 24 " pdb="HD22 ASN F 21 " model vdw 1.740 2.450 nonbonded pdb=" O GLY C 24 " pdb="HD22 ASN J 21 " model vdw 1.758 2.450 nonbonded pdb=" HZ PHE B 23 " pdb=" HD2 PHE F 15 " model vdw 1.855 2.100 nonbonded pdb=" HZ PHE E 23 " pdb=" HD2 PHE G 15 " model vdw 1.886 2.100 ... (remaining 49898 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.030 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.780 Find NCS groups from input model: 0.020 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4195 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 : 0.011 0.102 2075 Z= 0.779 Angle : 1.211 12.600 2815 Z= 0.607 Chirality : 0.067 0.257 330 Planarity : 0.008 0.025 370 Dihedral : 13.915 45.061 675 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.46 (0.35), residues: 250 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.26), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 11 TYR 0.018 0.004 TYR B 37 PHE 0.027 0.004 PHE C 15 HIS 0.010 0.004 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00795 ( 2065) covalent geometry : angle 1.21146 ( 2815) hydrogen bonds : bond 0.21651 ( 8) hydrogen bonds : angle 18.52809 ( 24) Misc. bond : bond 0.10119 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 18 HIS cc_start: 0.5073 (t-90) cc_final: 0.4361 (t-90) REVERT: F 27 LEU cc_start: 0.6517 (mt) cc_final: 0.6224 (mm) REVERT: H 22 ASN cc_start: 0.4329 (m110) cc_final: 0.4122 (m110) REVERT: H 32 VAL cc_start: 0.5757 (p) cc_final: 0.5456 (m) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1422 time to fit residues: 5.6447 Evaluate side-chains 33 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 21 ASN D 31 ASN ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5300 r_free = 0.5300 target = 0.301131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5227 r_free = 0.5227 target = 0.290289 restraints weight = 6010.462| |-----------------------------------------------------------------------------| r_work (start): 0.5218 rms_B_bonded: 1.63 r_work: 0.5173 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.5095 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.5095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4436 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2075 Z= 0.147 Angle : 0.578 5.348 2815 Z= 0.299 Chirality : 0.042 0.125 330 Planarity : 0.003 0.008 370 Dihedral : 6.306 19.222 275 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.43 % Allowed : 13.04 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.78 (0.32), residues: 250 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.25), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 11 TYR 0.014 0.002 TYR C 37 PHE 0.010 0.001 PHE H 15 HIS 0.006 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 2065) covalent geometry : angle 0.57846 ( 2815) hydrogen bonds : bond 0.06440 ( 8) hydrogen bonds : angle 17.61604 ( 24) Misc. bond : bond 0.00042 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 PHE cc_start: 0.4482 (m-10) cc_final: 0.4255 (m-10) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.1422 time to fit residues: 5.4701 Evaluate side-chains 32 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 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 = 0.5173 r_free = 0.5173 target = 0.282426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.274257 restraints weight = 5921.589| |-----------------------------------------------------------------------------| r_work (start): 0.5110 rms_B_bonded: 1.42 r_work: 0.5069 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.4996 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.4996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4677 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2075 Z= 0.250 Angle : 0.703 5.472 2815 Z= 0.391 Chirality : 0.042 0.129 330 Planarity : 0.005 0.024 370 Dihedral : 7.509 28.709 275 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 4.35 % Allowed : 11.74 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.83 (0.32), residues: 250 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.25), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 11 TYR 0.023 0.003 TYR C 37 PHE 0.016 0.002 PHE J 23 HIS 0.007 0.003 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 2065) covalent geometry : angle 0.70286 ( 2815) hydrogen bonds : bond 0.04786 ( 8) hydrogen bonds : angle 17.10800 ( 24) Misc. bond : bond 0.00039 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: K 27 LEU cc_start: 0.4277 (OUTLIER) cc_final: 0.3721 (mm) outliers start: 10 outliers final: 4 residues processed: 49 average time/residue: 0.2476 time to fit residues: 13.2622 Evaluate side-chains 46 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLN Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain K residue 27 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 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 = 0.5238 r_free = 0.5238 target = 0.287573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5182 r_free = 0.5182 target = 0.279858 restraints weight = 5827.296| |-----------------------------------------------------------------------------| r_work (start): 0.5176 rms_B_bonded: 1.21 r_work: 0.5126 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.5044 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.5044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4632 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2075 Z= 0.179 Angle : 0.580 5.134 2815 Z= 0.312 Chirality : 0.040 0.116 330 Planarity : 0.003 0.024 370 Dihedral : 6.740 25.493 275 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.20 % Favored : 86.80 % Rotamer: Outliers : 3.91 % Allowed : 13.91 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.93 (0.32), residues: 250 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.24), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 11 TYR 0.009 0.002 TYR E 37 PHE 0.010 0.001 PHE K 15 HIS 0.006 0.002 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 2065) covalent geometry : angle 0.57960 ( 2815) hydrogen bonds : bond 0.04733 ( 8) hydrogen bonds : angle 15.83526 ( 24) Misc. bond : bond 0.00032 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 LEU cc_start: 0.4582 (OUTLIER) cc_final: 0.4256 (pp) REVERT: J 37 TYR cc_start: 0.4999 (m-80) cc_final: 0.3765 (t80) REVERT: K 27 LEU cc_start: 0.3981 (OUTLIER) cc_final: 0.3485 (mm) outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 0.1883 time to fit residues: 10.1886 Evaluate side-chains 48 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain K residue 27 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5213 r_free = 0.5213 target = 0.279824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5148 r_free = 0.5148 target = 0.271131 restraints weight = 5937.125| |-----------------------------------------------------------------------------| r_work (start): 0.5147 rms_B_bonded: 1.39 r_work: 0.5100 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.5014 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.5014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4799 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 2075 Z= 0.291 Angle : 0.747 5.971 2815 Z= 0.414 Chirality : 0.042 0.119 330 Planarity : 0.005 0.025 370 Dihedral : 7.896 27.746 275 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.60 % Favored : 84.40 % Rotamer: Outliers : 6.09 % Allowed : 14.35 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.08 (0.32), residues: 250 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.24), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 11 TYR 0.019 0.003 TYR E 37 PHE 0.023 0.002 PHE J 23 HIS 0.009 0.003 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 2065) covalent geometry : angle 0.74679 ( 2815) hydrogen bonds : bond 0.04493 ( 8) hydrogen bonds : angle 16.18500 ( 24) Misc. bond : bond 0.00049 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: B 27 LEU cc_start: 0.4796 (OUTLIER) cc_final: 0.4440 (pp) outliers start: 14 outliers final: 8 residues processed: 47 average time/residue: 0.1845 time to fit residues: 9.6092 Evaluate side-chains 47 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain B residue 10 GLN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain J residue 35 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5272 r_free = 0.5272 target = 0.287291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5218 r_free = 0.5218 target = 0.279592 restraints weight = 5777.469| |-----------------------------------------------------------------------------| r_work (start): 0.5209 rms_B_bonded: 1.16 r_work: 0.5163 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.5077 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.5077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4661 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2075 Z= 0.161 Angle : 0.581 5.058 2815 Z= 0.310 Chirality : 0.040 0.117 330 Planarity : 0.003 0.022 370 Dihedral : 6.851 26.042 275 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.20 % Favored : 86.80 % Rotamer: Outliers : 4.35 % Allowed : 17.83 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.00 (0.32), residues: 250 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.24), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 11 TYR 0.012 0.001 TYR E 37 PHE 0.008 0.001 PHE F 23 HIS 0.009 0.002 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 2065) covalent geometry : angle 0.58139 ( 2815) hydrogen bonds : bond 0.04458 ( 8) hydrogen bonds : angle 15.16045 ( 24) Misc. bond : bond 0.00020 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.112 Fit side-chains REVERT: K 27 LEU cc_start: 0.4049 (OUTLIER) cc_final: 0.3557 (mm) outliers start: 10 outliers final: 8 residues processed: 40 average time/residue: 0.1793 time to fit residues: 7.9890 Evaluate side-chains 44 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain B residue 10 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain K residue 27 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN D 18 HIS F 18 HIS F 35 ASN G 18 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5299 r_free = 0.5299 target = 0.291344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5244 r_free = 0.5244 target = 0.283550 restraints weight = 5809.991| |-----------------------------------------------------------------------------| r_work (start): 0.5235 rms_B_bonded: 1.19 r_work: 0.5185 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.5100 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.5100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4611 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2075 Z= 0.131 Angle : 0.540 5.381 2815 Z= 0.281 Chirality : 0.040 0.121 330 Planarity : 0.003 0.019 370 Dihedral : 6.225 24.079 275 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.20 % Favored : 86.80 % Rotamer: Outliers : 4.35 % Allowed : 17.83 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.93 (0.33), residues: 250 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.25), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 11 TYR 0.009 0.001 TYR E 37 PHE 0.008 0.001 PHE H 23 HIS 0.008 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 2065) covalent geometry : angle 0.53989 ( 2815) hydrogen bonds : bond 0.05052 ( 8) hydrogen bonds : angle 14.37284 ( 24) Misc. bond : bond 0.00018 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: B 27 LEU cc_start: 0.4447 (OUTLIER) cc_final: 0.4067 (pp) REVERT: K 27 LEU cc_start: 0.3989 (OUTLIER) cc_final: 0.3524 (mm) outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 0.2528 time to fit residues: 12.3139 Evaluate side-chains 45 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain K residue 27 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5321 r_free = 0.5321 target = 0.293780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5268 r_free = 0.5268 target = 0.286311 restraints weight = 5730.142| |-----------------------------------------------------------------------------| r_work (start): 0.5262 rms_B_bonded: 1.10 r_work: 0.5215 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.5136 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.5136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4583 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2075 Z= 0.124 Angle : 0.529 5.085 2815 Z= 0.279 Chirality : 0.040 0.122 330 Planarity : 0.003 0.019 370 Dihedral : 6.117 23.653 275 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.20 % Favored : 86.80 % Rotamer: Outliers : 3.91 % Allowed : 18.70 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.91 (0.33), residues: 250 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.25), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 11 TYR 0.008 0.001 TYR E 37 PHE 0.011 0.001 PHE H 23 HIS 0.008 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 2065) covalent geometry : angle 0.52947 ( 2815) hydrogen bonds : bond 0.04642 ( 8) hydrogen bonds : angle 13.52468 ( 24) Misc. bond : bond 0.00016 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: B 27 LEU cc_start: 0.4425 (OUTLIER) cc_final: 0.4023 (pp) REVERT: K 27 LEU cc_start: 0.3832 (OUTLIER) cc_final: 0.3271 (mt) outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 0.1307 time to fit residues: 6.2019 Evaluate side-chains 44 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain K residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.0070 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5350 r_free = 0.5350 target = 0.298418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5294 r_free = 0.5294 target = 0.290597 restraints weight = 5677.021| |-----------------------------------------------------------------------------| r_work (start): 0.5288 rms_B_bonded: 1.15 r_work: 0.5238 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.5160 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.5160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4510 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2075 Z= 0.104 Angle : 0.507 5.080 2815 Z= 0.260 Chirality : 0.040 0.123 330 Planarity : 0.003 0.017 370 Dihedral : 5.635 22.562 275 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 3.04 % Allowed : 20.87 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.90 (0.34), residues: 250 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.26), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 11 TYR 0.006 0.001 TYR E 37 PHE 0.009 0.001 PHE H 23 HIS 0.008 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2065) covalent geometry : angle 0.50705 ( 2815) hydrogen bonds : bond 0.04866 ( 8) hydrogen bonds : angle 12.80334 ( 24) Misc. bond : bond 0.00011 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: K 27 LEU cc_start: 0.3708 (OUTLIER) cc_final: 0.3149 (mt) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.1650 time to fit residues: 7.6780 Evaluate side-chains 44 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain K residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.0270 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- 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 = 0.5321 r_free = 0.5321 target = 0.294698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5269 r_free = 0.5269 target = 0.287562 restraints weight = 5591.294| |-----------------------------------------------------------------------------| r_work (start): 0.5266 rms_B_bonded: 1.09 r_work: 0.5214 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.5137 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.5137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4558 moved from start: 0.6310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2075 Z= 0.125 Angle : 0.523 4.743 2815 Z= 0.274 Chirality : 0.040 0.124 330 Planarity : 0.003 0.017 370 Dihedral : 5.864 23.491 275 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 3.91 % Allowed : 20.00 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.94 (0.33), residues: 250 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.25), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 11 TYR 0.009 0.001 TYR E 37 PHE 0.008 0.001 PHE H 23 HIS 0.008 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 2065) covalent geometry : angle 0.52328 ( 2815) hydrogen bonds : bond 0.05147 ( 8) hydrogen bonds : angle 12.80668 ( 24) Misc. bond : bond 0.00017 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: B 27 LEU cc_start: 0.4535 (OUTLIER) cc_final: 0.4102 (pp) REVERT: K 27 LEU cc_start: 0.3632 (OUTLIER) cc_final: 0.3102 (mt) outliers start: 9 outliers final: 4 residues processed: 44 average time/residue: 0.2011 time to fit residues: 9.8037 Evaluate side-chains 44 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain K residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.294601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5276 r_free = 0.5276 target = 0.287585 restraints weight = 5685.549| |-----------------------------------------------------------------------------| r_work (start): 0.5272 rms_B_bonded: 1.07 r_work: 0.5221 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.5144 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.5144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4546 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2075 Z= 0.123 Angle : 0.520 5.090 2815 Z= 0.271 Chirality : 0.040 0.125 330 Planarity : 0.003 0.017 370 Dihedral : 5.834 23.565 275 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 3.91 % Allowed : 20.00 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.94 (0.33), residues: 250 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.25), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 11 TYR 0.008 0.001 TYR E 37 PHE 0.011 0.001 PHE C 23 HIS 0.007 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 2065) covalent geometry : angle 0.52044 ( 2815) hydrogen bonds : bond 0.04911 ( 8) hydrogen bonds : angle 12.73809 ( 24) Misc. bond : bond 0.00017 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1831.68 seconds wall clock time: 31 minutes 52.76 seconds (1912.76 seconds total)