Starting phenix.real_space_refine on Fri May 9 13:07:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8awt_15696/05_2025/8awt_15696.cif Found real_map, /net/cci-nas-00/data/ceres_data/8awt_15696/05_2025/8awt_15696.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/8awt_15696/05_2025/8awt_15696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8awt_15696/05_2025/8awt_15696.map" model { file = "/net/cci-nas-00/data/ceres_data/8awt_15696/05_2025/8awt_15696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8awt_15696/05_2025/8awt_15696.cif" } resolution = 3.0 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: 3 Type Number sf(0) Gaussians C 1190 2.51 5 N 340 2.21 5 O 380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 1910 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 190 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "A" 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: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.55, per 1000 atoms: 0.81 Number of scatterers: 1910 At special positions: 0 Unit cell: (67.5, 58.5, 43.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 380 8.00 N 340 7.00 C 1190 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 491.5 milliseconds 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 460 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 42.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 6.881A pdb=" N ASN A 14 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN C 14 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN E 14 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN G 14 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 22 removed outlier: 6.576A pdb=" N ASN A 21 " --> pdb=" O ASN C 22 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN C 21 " --> pdb=" O ASN E 22 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN E 21 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASN G 21 " --> pdb=" O ASN I 22 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 36 Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 18 removed outlier: 6.890A pdb=" N ASN B 14 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN D 14 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN F 14 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN H 14 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 21 through 22 removed outlier: 6.568A pdb=" N ASN B 21 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN D 21 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN F 21 " --> pdb=" O ASN H 22 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN H 21 " --> pdb=" O ASN J 22 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 36 72 hydrogen bonds defined for protein. 216 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: 0.43 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 310 1.29 - 1.35: 320 1.35 - 1.41: 220 1.41 - 1.48: 320 1.48 - 1.54: 760 Bond restraints: 1930 Sorted by residual: bond pdb=" CA VAL H 32 " pdb=" CB VAL H 32 " ideal model delta sigma weight residual 1.542 1.536 0.006 1.26e-02 6.30e+03 1.95e-01 bond pdb=" CA PHE A 15 " pdb=" CB PHE A 15 " ideal model delta sigma weight residual 1.535 1.527 0.008 2.02e-02 2.45e+03 1.64e-01 bond pdb=" CA PHE E 15 " pdb=" CB PHE E 15 " ideal model delta sigma weight residual 1.535 1.527 0.008 2.02e-02 2.45e+03 1.62e-01 bond pdb=" CA VAL B 32 " pdb=" CB VAL B 32 " ideal model delta sigma weight residual 1.542 1.537 0.005 1.26e-02 6.30e+03 1.61e-01 bond pdb=" CA VAL J 32 " pdb=" CB VAL J 32 " ideal model delta sigma weight residual 1.542 1.537 0.005 1.26e-02 6.30e+03 1.59e-01 ... (remaining 1925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.60: 2210 0.60 - 1.21: 348 1.21 - 1.81: 42 1.81 - 2.41: 10 2.41 - 3.01: 10 Bond angle restraints: 2620 Sorted by residual: angle pdb=" C PHE D 23 " pdb=" N GLY D 24 " pdb=" CA GLY D 24 " ideal model delta sigma weight residual 122.38 120.63 1.75 1.08e+00 8.57e-01 2.62e+00 angle pdb=" C PHE F 23 " pdb=" N GLY F 24 " pdb=" CA GLY F 24 " ideal model delta sigma weight residual 122.38 120.67 1.71 1.08e+00 8.57e-01 2.52e+00 angle pdb=" C PHE C 23 " pdb=" N GLY C 24 " pdb=" CA GLY C 24 " ideal model delta sigma weight residual 122.38 120.67 1.71 1.08e+00 8.57e-01 2.50e+00 angle pdb=" C PHE G 23 " pdb=" N GLY G 24 " pdb=" CA GLY G 24 " ideal model delta sigma weight residual 122.38 120.67 1.71 1.08e+00 8.57e-01 2.50e+00 angle pdb=" C PHE I 23 " pdb=" N GLY I 24 " pdb=" CA GLY I 24 " ideal model delta sigma weight residual 122.38 120.68 1.70 1.08e+00 8.57e-01 2.46e+00 ... (remaining 2615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.25: 930 8.25 - 16.50: 95 16.50 - 24.74: 15 24.74 - 32.99: 10 32.99 - 41.24: 10 Dihedral angle restraints: 1060 sinusoidal: 340 harmonic: 720 Sorted by residual: dihedral pdb=" N PHE B 15 " pdb=" CA PHE B 15 " pdb=" CB PHE B 15 " pdb=" CG PHE B 15 " ideal model delta sinusoidal sigma weight residual -180.00 -147.71 -32.29 3 1.50e+01 4.44e-03 5.31e+00 dihedral pdb=" N PHE D 15 " pdb=" CA PHE D 15 " pdb=" CB PHE D 15 " pdb=" CG PHE D 15 " ideal model delta sinusoidal sigma weight residual -180.00 -147.71 -32.29 3 1.50e+01 4.44e-03 5.31e+00 dihedral pdb=" N PHE J 15 " pdb=" CA PHE J 15 " pdb=" CB PHE J 15 " pdb=" CG PHE J 15 " ideal model delta sinusoidal sigma weight residual 180.00 -147.72 -32.28 3 1.50e+01 4.44e-03 5.30e+00 ... (remaining 1057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 176 0.024 - 0.047: 98 0.047 - 0.071: 6 0.071 - 0.094: 0 0.094 - 0.118: 30 Chirality restraints: 310 Sorted by residual: chirality pdb=" CA ILE A 26 " pdb=" N ILE A 26 " pdb=" C ILE A 26 " pdb=" CB ILE A 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE C 26 " pdb=" N ILE C 26 " pdb=" C ILE C 26 " pdb=" CB ILE C 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 chirality pdb=" CA ILE I 26 " pdb=" N ILE I 26 " pdb=" C ILE I 26 " pdb=" CB ILE I 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 307 not shown) Planarity restraints: 340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 23 " 0.004 2.00e-02 2.50e+03 3.11e-03 1.69e-01 pdb=" CG PHE I 23 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE I 23 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE I 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE I 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE I 23 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE I 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 23 " 0.004 2.00e-02 2.50e+03 3.10e-03 1.68e-01 pdb=" CG PHE D 23 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE D 23 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 23 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 23 " 0.004 2.00e-02 2.50e+03 3.09e-03 1.67e-01 pdb=" CG PHE F 23 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE F 23 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE F 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE F 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 23 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 23 " 0.002 2.00e-02 2.50e+03 ... (remaining 337 not shown) Histogram of nonbonded interaction distances: 2.67 - 3.12: 1353 3.12 - 3.56: 1726 3.56 - 4.01: 2618 4.01 - 4.45: 3512 4.45 - 4.90: 5711 Nonbonded interactions: 14920 Sorted by model distance: nonbonded pdb=" N ALA E 13 " pdb=" O ALA E 13 " model vdw 2.671 2.496 nonbonded pdb=" N ALA A 13 " pdb=" O ALA A 13 " model vdw 2.671 2.496 nonbonded pdb=" N ALA I 13 " pdb=" O ALA I 13 " model vdw 2.672 2.496 nonbonded pdb=" N ALA G 13 " pdb=" O ALA G 13 " model vdw 2.672 2.496 nonbonded pdb=" N ALA C 13 " pdb=" O ALA C 13 " model vdw 2.672 2.496 ... (remaining 14915 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.630 Find NCS groups from input model: 0.050 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:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.008 0.102 1940 Z= 0.743 Angle : 0.471 3.013 2620 Z= 0.276 Chirality : 0.040 0.118 310 Planarity : 0.001 0.003 340 Dihedral : 9.301 41.237 600 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.11 (0.21), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.16), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 18 PHE 0.007 0.002 PHE H 23 TYR 0.001 0.000 TYR F 37 Details of bonding type rmsd hydrogen bonds : bond 0.19894 ( 72) hydrogen bonds : angle 6.43401 ( 216) covalent geometry : bond 0.00300 ( 1930) covalent geometry : angle 0.47112 ( 2620) Misc. bond : bond 0.10128 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1814 time to fit residues: 5.6013 Evaluate side-chains 0 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 35 ASN C 21 ASN D 21 ASN E 35 ASN F 21 ASN H 21 ASN I 21 ASN J 21 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.082756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.061884 restraints weight = 2744.542| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.65 r_work: 0.2749 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 1940 Z= 0.173 Angle : 0.510 6.152 2620 Z= 0.260 Chirality : 0.042 0.114 310 Planarity : 0.002 0.008 340 Dihedral : 4.344 13.079 260 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % 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: -3.96 (0.25), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.19), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 18 PHE 0.011 0.002 PHE G 23 TYR 0.003 0.001 TYR I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04946 ( 72) hydrogen bonds : angle 4.53234 ( 216) covalent geometry : bond 0.00367 ( 1930) covalent geometry : angle 0.51049 ( 2620) Misc. bond : bond 0.00013 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.189 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.2138 time to fit residues: 0.9834 Evaluate side-chains 1 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.083846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.061994 restraints weight = 2735.758| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.73 r_work: 0.2827 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 1940 Z= 0.107 Angle : 0.429 4.696 2620 Z= 0.217 Chirality : 0.041 0.115 310 Planarity : 0.001 0.005 340 Dihedral : 3.894 11.794 260 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % 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: -3.78 (0.29), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.22), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 18 PHE 0.007 0.001 PHE J 23 TYR 0.002 0.000 TYR C 37 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 72) hydrogen bonds : angle 4.10934 ( 216) covalent geometry : bond 0.00219 ( 1930) covalent geometry : angle 0.42939 ( 2620) Misc. bond : bond 0.00004 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.1989 time to fit residues: 0.9722 Evaluate side-chains 1 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.060712 restraints weight = 2677.584| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.73 r_work: 0.2777 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1940 Z= 0.201 Angle : 0.491 6.028 2620 Z= 0.255 Chirality : 0.040 0.117 310 Planarity : 0.002 0.005 340 Dihedral : 4.334 12.495 260 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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: -3.85 (0.30), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.23), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 18 PHE 0.012 0.002 PHE B 23 TYR 0.003 0.001 TYR I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 72) hydrogen bonds : angle 4.33686 ( 216) covalent geometry : bond 0.00434 ( 1930) covalent geometry : angle 0.49138 ( 2620) Misc. bond : bond 0.00014 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.229 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3901 Evaluate side-chains 0 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.084641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.061194 restraints weight = 2680.774| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.73 r_work: 0.2794 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 1940 Z= 0.164 Angle : 0.461 4.977 2620 Z= 0.240 Chirality : 0.040 0.116 310 Planarity : 0.002 0.005 340 Dihedral : 4.175 12.519 260 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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: -3.85 (0.32), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 18 PHE 0.010 0.002 PHE B 23 TYR 0.002 0.001 TYR I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 72) hydrogen bonds : angle 4.25777 ( 216) covalent geometry : bond 0.00352 ( 1930) covalent geometry : angle 0.46102 ( 2620) Misc. bond : bond 0.00004 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.214 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3401 Evaluate side-chains 0 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 HIS J 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.060001 restraints weight = 2761.680| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.74 r_work: 0.2778 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 1940 Z= 0.237 Angle : 0.501 5.231 2620 Z= 0.267 Chirality : 0.041 0.115 310 Planarity : 0.002 0.006 340 Dihedral : 4.492 12.588 260 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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: -3.98 (0.31), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 18 PHE 0.013 0.002 PHE J 23 TYR 0.003 0.001 TYR H 37 Details of bonding type rmsd hydrogen bonds : bond 0.05121 ( 72) hydrogen bonds : angle 4.48585 ( 216) covalent geometry : bond 0.00519 ( 1930) covalent geometry : angle 0.50146 ( 2620) Misc. bond : bond 0.00031 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.228 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4337 Evaluate side-chains 0 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.3263 r_free = 0.3263 target = 0.084184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.060612 restraints weight = 2734.363| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.73 r_work: 0.2781 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 1940 Z= 0.174 Angle : 0.460 4.759 2620 Z= 0.242 Chirality : 0.040 0.116 310 Planarity : 0.002 0.005 340 Dihedral : 4.231 12.149 260 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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: -3.99 (0.32), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.25), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 18 PHE 0.011 0.002 PHE G 23 TYR 0.002 0.001 TYR I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 72) hydrogen bonds : angle 4.36503 ( 216) covalent geometry : bond 0.00376 ( 1930) covalent geometry : angle 0.46023 ( 2620) Misc. bond : bond 0.00027 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.188 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3141 Evaluate side-chains 0 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3308 r_free = 0.3308 target = 0.086597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.062754 restraints weight = 2787.831| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.78 r_work: 0.2842 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.007 1940 Z= 0.076 Angle : 0.399 4.227 2620 Z= 0.203 Chirality : 0.041 0.113 310 Planarity : 0.001 0.004 340 Dihedral : 3.692 11.286 260 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % 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: -3.93 (0.32), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.25), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 18 PHE 0.005 0.001 PHE G 23 TYR 0.001 0.000 TYR I 37 Details of bonding type rmsd hydrogen bonds : bond 0.02603 ( 72) hydrogen bonds : angle 4.07056 ( 216) covalent geometry : bond 0.00150 ( 1930) covalent geometry : angle 0.39936 ( 2620) Misc. bond : bond 0.00009 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.233 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.2054 time to fit residues: 1.2251 Evaluate side-chains 1 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN G 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.059717 restraints weight = 2922.173| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.75 r_work: 0.2765 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.028 1940 Z= 0.311 Angle : 0.548 6.630 2620 Z= 0.295 Chirality : 0.042 0.117 310 Planarity : 0.003 0.007 340 Dihedral : 4.592 12.975 260 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % 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: -4.08 (0.32), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 18 PHE 0.017 0.003 PHE D 23 TYR 0.004 0.001 TYR I 37 Details of bonding type rmsd hydrogen bonds : bond 0.05643 ( 72) hydrogen bonds : angle 4.46895 ( 216) covalent geometry : bond 0.00683 ( 1930) covalent geometry : angle 0.54784 ( 2620) Misc. bond : bond 0.00042 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.216 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.3359 time to fit residues: 1.3994 Evaluate side-chains 0 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.061645 restraints weight = 2750.405| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.74 r_work: 0.2816 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 1940 Z= 0.121 Angle : 0.440 6.020 2620 Z= 0.227 Chirality : 0.040 0.113 310 Planarity : 0.001 0.004 340 Dihedral : 4.029 11.577 260 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % 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: -4.04 (0.32), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.25), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.008 0.001 PHE G 23 TYR 0.002 0.000 TYR I 37 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 72) hydrogen bonds : angle 4.31409 ( 216) covalent geometry : bond 0.00254 ( 1930) covalent geometry : angle 0.44021 ( 2620) Misc. bond : bond 0.00016 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.197 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.2223 time to fit residues: 0.5498 Evaluate side-chains 0 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 0.0370 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.084883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.061114 restraints weight = 2751.201| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.72 r_work: 0.2789 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1940 Z= 0.160 Angle : 0.460 6.015 2620 Z= 0.241 Chirality : 0.040 0.114 310 Planarity : 0.002 0.005 340 Dihedral : 4.166 11.768 260 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % 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: -4.02 (0.32), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.25), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 18 PHE 0.010 0.002 PHE G 23 TYR 0.002 0.001 TYR I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 72) hydrogen bonds : angle 4.39362 ( 216) covalent geometry : bond 0.00345 ( 1930) covalent geometry : angle 0.46034 ( 2620) Misc. bond : bond 0.00021 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1342.65 seconds wall clock time: 24 minutes 8.86 seconds (1448.86 seconds total)