Starting phenix.real_space_refine on Fri May 9 12:42:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qn7_18509/05_2025/8qn7_18509.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qn7_18509/05_2025/8qn7_18509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qn7_18509/05_2025/8qn7_18509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qn7_18509/05_2025/8qn7_18509.map" model { file = "/net/cci-nas-00/data/ceres_data/8qn7_18509/05_2025/8qn7_18509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qn7_18509/05_2025/8qn7_18509.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 920 2.51 5 N 255 2.21 5 O 275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 1455 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 291 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Restraints were copied for chains: C, B, E, D Time building chain proxies: 0.99, per 1000 atoms: 0.68 Number of scatterers: 1455 At special positions: 0 Unit cell: (82.584, 72.168, 29.76, 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) S 5 16.00 O 275 8.00 N 255 7.00 C 920 6.00 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=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 179.9 milliseconds 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 355 1.33 - 1.45: 410 1.45 - 1.58: 710 1.58 - 1.70: 0 1.70 - 1.82: 10 Bond restraints: 1485 Sorted by residual: bond pdb=" CA SER B 8 " pdb=" CB SER B 8 " ideal model delta sigma weight residual 1.530 1.487 0.043 1.48e-02 4.57e+03 8.27e+00 bond pdb=" CA SER C 8 " pdb=" CB SER C 8 " ideal model delta sigma weight residual 1.530 1.487 0.042 1.48e-02 4.57e+03 8.22e+00 bond pdb=" CA SER A 8 " pdb=" CB SER A 8 " ideal model delta sigma weight residual 1.530 1.487 0.042 1.48e-02 4.57e+03 8.15e+00 bond pdb=" CA SER E 8 " pdb=" CB SER E 8 " ideal model delta sigma weight residual 1.530 1.487 0.042 1.48e-02 4.57e+03 8.15e+00 bond pdb=" CA SER D 8 " pdb=" CB SER D 8 " ideal model delta sigma weight residual 1.530 1.488 0.041 1.48e-02 4.57e+03 7.81e+00 ... (remaining 1480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 1213 1.08 - 2.17: 553 2.17 - 3.25: 146 3.25 - 4.33: 43 4.33 - 5.42: 30 Bond angle restraints: 1985 Sorted by residual: angle pdb=" CA HIS E 13 " pdb=" CB HIS E 13 " pdb=" CG HIS E 13 " ideal model delta sigma weight residual 113.80 118.98 -5.18 1.00e+00 1.00e+00 2.69e+01 angle pdb=" CA HIS A 13 " pdb=" CB HIS A 13 " pdb=" CG HIS A 13 " ideal model delta sigma weight residual 113.80 118.98 -5.18 1.00e+00 1.00e+00 2.68e+01 angle pdb=" CA HIS C 13 " pdb=" CB HIS C 13 " pdb=" CG HIS C 13 " ideal model delta sigma weight residual 113.80 118.97 -5.17 1.00e+00 1.00e+00 2.68e+01 angle pdb=" CA HIS B 13 " pdb=" CB HIS B 13 " pdb=" CG HIS B 13 " ideal model delta sigma weight residual 113.80 118.97 -5.17 1.00e+00 1.00e+00 2.68e+01 angle pdb=" CA HIS D 13 " pdb=" CB HIS D 13 " pdb=" CG HIS D 13 " ideal model delta sigma weight residual 113.80 118.96 -5.16 1.00e+00 1.00e+00 2.67e+01 ... (remaining 1980 not shown) Histogram of dihedral angle deviations from ideal: 0.04 - 11.62: 709 11.62 - 23.19: 76 23.19 - 34.77: 25 34.77 - 46.35: 15 46.35 - 57.93: 5 Dihedral angle restraints: 830 sinusoidal: 320 harmonic: 510 Sorted by residual: dihedral pdb=" CA GLU D 22 " pdb=" C GLU D 22 " pdb=" N ASP D 23 " pdb=" CA ASP D 23 " ideal model delta harmonic sigma weight residual -180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA GLU E 22 " pdb=" C GLU E 22 " pdb=" N ASP E 23 " pdb=" CA ASP E 23 " ideal model delta harmonic sigma weight residual 180.00 -164.01 -15.99 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA GLU A 22 " pdb=" C GLU A 22 " pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta harmonic sigma weight residual -180.00 -164.01 -15.99 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 827 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.042: 60 0.042 - 0.082: 54 0.082 - 0.123: 61 0.123 - 0.163: 15 0.163 - 0.204: 10 Chirality restraints: 200 Sorted by residual: chirality pdb=" CA HIS B 14 " pdb=" N HIS B 14 " pdb=" C HIS B 14 " pdb=" CB HIS B 14 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA HIS E 14 " pdb=" N HIS E 14 " pdb=" C HIS E 14 " pdb=" CB HIS E 14 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA HIS D 14 " pdb=" N HIS D 14 " pdb=" C HIS D 14 " pdb=" CB HIS D 14 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 197 not shown) Planarity restraints: 265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 25 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C GLY E 25 " 0.026 2.00e-02 2.50e+03 pdb=" O GLY E 25 " -0.010 2.00e-02 2.50e+03 pdb=" N SER E 26 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 25 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C GLY B 25 " 0.026 2.00e-02 2.50e+03 pdb=" O GLY B 25 " -0.010 2.00e-02 2.50e+03 pdb=" N SER B 26 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 25 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C GLY C 25 " -0.026 2.00e-02 2.50e+03 pdb=" O GLY C 25 " 0.010 2.00e-02 2.50e+03 pdb=" N SER C 26 " 0.009 2.00e-02 2.50e+03 ... (remaining 262 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 779 3.04 - 3.50: 1239 3.50 - 3.97: 2210 3.97 - 4.43: 2481 4.43 - 4.90: 4512 Nonbonded interactions: 11221 Sorted by model distance: nonbonded pdb=" NZ LYS A 16 " pdb=" OE1 GLU B 11 " model vdw 2.570 3.120 nonbonded pdb=" OE1 GLU A 11 " pdb=" NZ LYS E 16 " model vdw 2.570 3.120 nonbonded pdb=" OE1 GLU C 11 " pdb=" NZ LYS D 16 " model vdw 2.570 3.120 nonbonded pdb=" N ALA B 30 " pdb=" O ALA B 30 " model vdw 2.652 2.496 nonbonded pdb=" N ALA C 30 " pdb=" O ALA C 30 " model vdw 2.653 2.496 ... (remaining 11216 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 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 1.590 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.390 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 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 : 0.010 0.043 1485 Z= 0.647 Angle : 1.434 5.419 1985 Z= 0.986 Chirality : 0.087 0.204 200 Planarity : 0.010 0.058 265 Dihedral : 13.541 57.925 510 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.45 % Allowed : 0.00 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.33), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.25), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.006 HIS D 13 PHE 0.016 0.007 PHE A 19 TYR 0.006 0.003 TYR E 10 ARG 0.006 0.003 ARG B 5 Details of bonding type rmsd covalent geometry : bond 0.00966 ( 1485) covalent geometry : angle 1.43395 ( 1985) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.215 Fit side-chains REVERT: C 3 GLU cc_start: 0.8908 (tt0) cc_final: 0.8218 (tm-30) REVERT: E 3 GLU cc_start: 0.8847 (tt0) cc_final: 0.8167 (tm-30) outliers start: 5 outliers final: 0 residues processed: 52 average time/residue: 1.2455 time to fit residues: 65.7786 Evaluate side-chains 40 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS B 14 HIS C 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.137173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.119688 restraints weight = 1542.931| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.19 r_work: 0.3581 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 1485 Z= 0.204 Angle : 0.638 4.342 1985 Z= 0.336 Chirality : 0.051 0.112 200 Planarity : 0.002 0.017 265 Dihedral : 5.620 16.560 195 Min Nonbonded Distance : 2.696 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.69 % Allowed : 6.21 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.37), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.28), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS C 13 PHE 0.008 0.002 PHE D 19 TYR 0.004 0.001 TYR A 10 ARG 0.002 0.000 ARG A 5 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 1485) covalent geometry : angle 0.63773 ( 1985) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.138 Fit side-chains REVERT: A 3 GLU cc_start: 0.8400 (tt0) cc_final: 0.8149 (mt-10) REVERT: D 3 GLU cc_start: 0.8347 (tt0) cc_final: 0.7934 (mt-10) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 1.4370 time to fit residues: 63.9776 Evaluate side-chains 44 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS E 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.134362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.117141 restraints weight = 1583.471| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.18 r_work: 0.3555 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 1485 Z= 0.235 Angle : 0.629 4.331 1985 Z= 0.328 Chirality : 0.051 0.115 200 Planarity : 0.002 0.018 265 Dihedral : 5.639 16.976 195 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.69 % Allowed : 10.34 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.39), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.30), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 13 PHE 0.009 0.002 PHE D 19 TYR 0.007 0.001 TYR C 10 ARG 0.001 0.000 ARG D 5 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 1485) covalent geometry : angle 0.62905 ( 1985) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.169 Fit side-chains REVERT: A 3 GLU cc_start: 0.8398 (tt0) cc_final: 0.8044 (mt-10) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 1.4437 time to fit residues: 64.2960 Evaluate side-chains 43 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.135679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.118722 restraints weight = 1535.615| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.14 r_work: 0.3569 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 1485 Z= 0.186 Angle : 0.555 3.920 1985 Z= 0.290 Chirality : 0.050 0.116 200 Planarity : 0.002 0.014 265 Dihedral : 5.408 16.643 195 Min Nonbonded Distance : 2.688 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.07 % Allowed : 11.72 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.40), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 13 PHE 0.008 0.001 PHE D 19 TYR 0.005 0.001 TYR E 10 ARG 0.001 0.000 ARG E 5 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 1485) covalent geometry : angle 0.55517 ( 1985) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.156 Fit side-chains REVERT: A 3 GLU cc_start: 0.8388 (tt0) cc_final: 0.8038 (mt-10) outliers start: 3 outliers final: 0 residues processed: 45 average time/residue: 1.5651 time to fit residues: 71.2414 Evaluate side-chains 43 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 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 = 0.3923 r_free = 0.3923 target = 0.139206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.122247 restraints weight = 1483.636| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.12 r_work: 0.3616 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1485 Z= 0.112 Angle : 0.454 3.161 1985 Z= 0.241 Chirality : 0.049 0.119 200 Planarity : 0.001 0.010 265 Dihedral : 5.003 15.824 195 Min Nonbonded Distance : 2.687 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.45 % Allowed : 10.34 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.006 0.001 PHE B 19 TYR 0.005 0.001 TYR E 10 ARG 0.001 0.000 ARG B 5 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 1485) covalent geometry : angle 0.45418 ( 1985) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.154 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 47 average time/residue: 1.6203 time to fit residues: 76.9529 Evaluate side-chains 42 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.133870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.116485 restraints weight = 1548.445| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.17 r_work: 0.3537 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 1485 Z= 0.235 Angle : 0.609 4.258 1985 Z= 0.316 Chirality : 0.051 0.116 200 Planarity : 0.002 0.019 265 Dihedral : 5.399 16.896 195 Min Nonbonded Distance : 2.685 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.45 % Allowed : 10.34 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 13 PHE 0.010 0.002 PHE E 19 TYR 0.004 0.001 TYR E 10 ARG 0.001 0.000 ARG E 5 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 1485) covalent geometry : angle 0.60854 ( 1985) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.170 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 47 average time/residue: 1.7369 time to fit residues: 82.5422 Evaluate side-chains 44 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 3 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.137827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.120511 restraints weight = 1554.097| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.17 r_work: 0.3593 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 1485 Z= 0.127 Angle : 0.479 3.396 1985 Z= 0.252 Chirality : 0.049 0.118 200 Planarity : 0.001 0.011 265 Dihedral : 5.026 16.236 195 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.76 % Allowed : 11.03 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.42), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.32), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.006 0.001 PHE D 19 TYR 0.005 0.001 TYR E 10 ARG 0.001 0.000 ARG E 5 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 1485) covalent geometry : angle 0.47900 ( 1985) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.157 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 46 average time/residue: 1.6555 time to fit residues: 76.9567 Evaluate side-chains 42 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 5 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 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 = 0.3909 r_free = 0.3909 target = 0.137143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.120005 restraints weight = 1517.721| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.14 r_work: 0.3592 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 1485 Z= 0.136 Angle : 0.488 3.493 1985 Z= 0.257 Chirality : 0.049 0.118 200 Planarity : 0.002 0.012 265 Dihedral : 4.995 16.086 195 Min Nonbonded Distance : 2.687 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.07 % Allowed : 11.72 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.42), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.32), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 13 PHE 0.007 0.001 PHE A 19 TYR 0.004 0.001 TYR E 10 ARG 0.001 0.000 ARG E 5 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 1485) covalent geometry : angle 0.48815 ( 1985) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.175 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 1.5870 time to fit residues: 72.1972 Evaluate side-chains 43 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.133725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.116434 restraints weight = 1578.434| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.17 r_work: 0.3543 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 1485 Z= 0.245 Angle : 0.624 4.397 1985 Z= 0.324 Chirality : 0.051 0.117 200 Planarity : 0.002 0.022 265 Dihedral : 5.362 17.091 195 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.38 % Allowed : 13.79 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 13 PHE 0.011 0.002 PHE E 19 TYR 0.004 0.001 TYR B 10 ARG 0.001 0.000 ARG E 5 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 1485) covalent geometry : angle 0.62437 ( 1985) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.167 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 44 average time/residue: 1.6060 time to fit residues: 71.4393 Evaluate side-chains 44 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 22 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 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 = 0.3937 r_free = 0.3937 target = 0.139656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.122745 restraints weight = 1527.833| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.11 r_work: 0.3635 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 1485 Z= 0.094 Angle : 0.433 3.094 1985 Z= 0.231 Chirality : 0.049 0.120 200 Planarity : 0.001 0.007 265 Dihedral : 4.828 15.855 195 Min Nonbonded Distance : 2.688 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.38 % Allowed : 13.79 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.32), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.005 0.001 PHE D 19 TYR 0.006 0.001 TYR E 10 ARG 0.001 0.000 ARG B 5 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 1485) covalent geometry : angle 0.43341 ( 1985) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.155 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 1.5636 time to fit residues: 69.5550 Evaluate side-chains 41 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 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 = 0.3900 r_free = 0.3900 target = 0.136785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.119426 restraints weight = 1582.885| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.19 r_work: 0.3585 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 1485 Z= 0.143 Angle : 0.494 3.574 1985 Z= 0.261 Chirality : 0.050 0.119 200 Planarity : 0.002 0.013 265 Dihedral : 4.948 15.969 195 Min Nonbonded Distance : 2.687 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.07 % Allowed : 13.79 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 13 PHE 0.007 0.001 PHE D 19 TYR 0.006 0.001 TYR E 10 ARG 0.001 0.000 ARG E 5 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 1485) covalent geometry : angle 0.49378 ( 1985) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1970.03 seconds wall clock time: 34 minutes 41.66 seconds (2081.66 seconds total)