Starting phenix.real_space_refine on Wed Jul 23 07:48:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az0_15728/07_2025/8az0_15728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az0_15728/07_2025/8az0_15728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8az0_15728/07_2025/8az0_15728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az0_15728/07_2025/8az0_15728.map" model { file = "/net/cci-nas-00/data/ceres_data/8az0_15728/07_2025/8az0_15728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az0_15728/07_2025/8az0_15728.cif" } resolution = 3.4 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= 0.003 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 1350 2.51 5 N 420 2.21 5 O 410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2180 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 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: 1.46, per 1000 atoms: 0.67 Number of scatterers: 2180 At special positions: 0 Unit cell: (63, 73.08, 45.36, 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 410 8.00 N 420 7.00 C 1350 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: 0.50 Conformation dependent library (CDL) restraints added in 458.1 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 53.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 22 removed outlier: 6.969A pdb=" N ASN A 21 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN C 22 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN C 21 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN E 22 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN E 21 " --> pdb=" O GLY G 20 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASN G 22 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN G 21 " --> pdb=" O GLY I 20 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN I 22 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.413A pdb=" N SER A 29 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL C 32 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASN A 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER C 29 " --> pdb=" O THR E 30 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL E 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN C 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER E 29 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL G 32 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN E 31 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER G 29 " --> pdb=" O THR I 30 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL I 32 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN G 31 " --> pdb=" O VAL I 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 22 removed outlier: 6.991A pdb=" N ASN B 21 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASN D 22 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN D 21 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN F 22 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN F 21 " --> pdb=" O GLY H 20 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN H 22 " --> pdb=" O ASN F 21 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN H 21 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN J 22 " --> pdb=" O ASN H 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.397A pdb=" N SER B 29 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL D 32 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN B 31 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER D 29 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL F 32 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN D 31 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER F 29 " --> pdb=" O THR H 30 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL H 32 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN F 31 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER H 29 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL J 32 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN H 31 " --> pdb=" O VAL J 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 80 hydrogen bonds defined for protein. 232 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: 0.51 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 340 1.29 - 1.35: 400 1.35 - 1.41: 270 1.41 - 1.48: 306 1.48 - 1.54: 904 Bond restraints: 2220 Sorted by residual: bond pdb=" N THR G 36 " pdb=" CA THR G 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.76e+00 bond pdb=" N THR J 36 " pdb=" CA THR J 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.73e+00 bond pdb=" N THR B 36 " pdb=" CA THR B 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.68e+00 bond pdb=" N THR H 36 " pdb=" CA THR H 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.62e+00 bond pdb=" N THR E 36 " pdb=" CA THR E 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.62e+00 ... (remaining 2215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 2678 0.92 - 1.84: 200 1.84 - 2.76: 102 2.76 - 3.68: 30 3.68 - 4.60: 10 Bond angle restraints: 3020 Sorted by residual: angle pdb=" CA SER B 34 " pdb=" C SER B 34 " pdb=" O SER B 34 " ideal model delta sigma weight residual 121.28 117.78 3.50 1.19e+00 7.06e-01 8.64e+00 angle pdb=" CA SER A 34 " pdb=" C SER A 34 " pdb=" O SER A 34 " ideal model delta sigma weight residual 121.28 117.80 3.48 1.19e+00 7.06e-01 8.57e+00 angle pdb=" CA SER J 34 " pdb=" C SER J 34 " pdb=" O SER J 34 " ideal model delta sigma weight residual 121.28 117.81 3.47 1.19e+00 7.06e-01 8.49e+00 angle pdb=" CA SER G 34 " pdb=" C SER G 34 " pdb=" O SER G 34 " ideal model delta sigma weight residual 121.28 117.81 3.47 1.19e+00 7.06e-01 8.49e+00 angle pdb=" CA SER D 34 " pdb=" C SER D 34 " pdb=" O SER D 34 " ideal model delta sigma weight residual 121.28 117.83 3.45 1.19e+00 7.06e-01 8.42e+00 ... (remaining 3015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.96: 1022 5.96 - 11.92: 128 11.92 - 17.87: 72 17.87 - 23.83: 28 23.83 - 29.79: 10 Dihedral angle restraints: 1260 sinusoidal: 440 harmonic: 820 Sorted by residual: dihedral pdb=" N HIS J 18 " pdb=" CA AHIS J 18 " pdb=" CB AHIS J 18 " pdb=" CG AHIS J 18 " ideal model delta sinusoidal sigma weight residual -60.00 -83.02 23.02 3 1.50e+01 4.44e-03 3.05e+00 dihedral pdb=" N HIS E 18 " pdb=" CA AHIS E 18 " pdb=" CB AHIS E 18 " pdb=" CG AHIS E 18 " ideal model delta sinusoidal sigma weight residual -60.00 -83.00 23.00 3 1.50e+01 4.44e-03 3.04e+00 dihedral pdb=" N HIS D 18 " pdb=" CA AHIS D 18 " pdb=" CB AHIS D 18 " pdb=" CG AHIS D 18 " ideal model delta sinusoidal sigma weight residual -60.00 -82.99 22.99 3 1.50e+01 4.44e-03 3.04e+00 ... (remaining 1257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 127 0.027 - 0.054: 149 0.054 - 0.080: 24 0.080 - 0.107: 17 0.107 - 0.134: 23 Chirality restraints: 340 Sorted by residual: chirality pdb=" CA ILE F 26 " pdb=" N ILE F 26 " pdb=" C ILE F 26 " pdb=" CB ILE F 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE B 26 " pdb=" N ILE B 26 " pdb=" C ILE B 26 " pdb=" CB ILE B 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-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 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 337 not shown) Planarity restraints: 400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 32 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" C VAL D 32 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL D 32 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY D 33 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 32 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C VAL B 32 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL B 32 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY B 33 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 32 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" C VAL I 32 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL I 32 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY I 33 " 0.017 2.00e-02 2.50e+03 ... (remaining 397 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 1471 3.07 - 3.53: 1993 3.53 - 3.98: 3105 3.98 - 4.44: 3846 4.44 - 4.90: 7332 Nonbonded interactions: 17747 Sorted by model distance: nonbonded pdb=" O SER B 34 " pdb=" OG SER B 34 " model vdw 2.611 3.040 nonbonded pdb=" O SER J 34 " pdb=" OG SER J 34 " model vdw 2.612 3.040 nonbonded pdb=" O SER F 34 " pdb=" OG SER F 34 " model vdw 2.612 3.040 nonbonded pdb=" O SER H 34 " pdb=" OG SER H 34 " model vdw 2.612 3.040 nonbonded pdb=" O SER D 34 " pdb=" OG SER D 34 " model vdw 2.612 3.040 ... (remaining 17742 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=0.50 max=1.00 mean=0.97 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: 1.140 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: 0.020 Set scattering table: 0.020 Process input model: 10.320 Find NCS groups from input model: 0.060 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.009 0.096 2230 Z= 0.729 Angle : 0.742 4.601 3020 Z= 0.491 Chirality : 0.051 0.134 340 Planarity : 0.005 0.030 400 Dihedral : 8.049 29.789 740 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -4.46 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 23 TYR 0.003 0.001 TYR E 37 ARG 0.000 0.000 ARG E 11 Details of bonding type rmsd hydrogen bonds : bond 0.16649 ( 80) hydrogen bonds : angle 8.05042 ( 232) covalent geometry : bond 0.00582 ( 2220) covalent geometry : angle 0.74198 ( 3020) Misc. bond : bond 0.09481 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.275 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0720 time to fit residues: 1.5233 Evaluate side-chains 13 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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: 3.9990 chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A A 21 ASN B 18 HIS A B 21 ASN C 18 HIS A C 21 ASN D 18 HIS A D 21 ASN E 18 HIS A E 21 ASN F 18 HIS A F 21 ASN G 18 HIS A G 21 ASN H 18 HIS A H 21 ASN I 18 HIS A I 21 ASN J 18 HIS A J 21 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.106645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.083929 restraints weight = 17686.805| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 5.11 r_work: 0.3088 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 2230 Z= 0.117 Angle : 0.381 2.754 3020 Z= 0.224 Chirality : 0.043 0.125 340 Planarity : 0.002 0.005 400 Dihedral : 3.589 7.198 310 Min Nonbonded Distance : 2.687 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -4.47 (0.28), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.21), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE H 15 TYR 0.002 0.001 TYR G 37 ARG 0.001 0.000 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 80) hydrogen bonds : angle 4.86057 ( 232) covalent geometry : bond 0.00257 ( 2220) covalent geometry : angle 0.38075 ( 3020) Misc. bond : bond 0.00039 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.227 Fit side-chains REVERT: G 19 SER cc_start: 0.8702 (t) cc_final: 0.8308 (p) REVERT: H 19 SER cc_start: 0.8660 (t) cc_final: 0.8323 (p) REVERT: I 19 SER cc_start: 0.8937 (t) cc_final: 0.8706 (p) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0671 time to fit residues: 2.4449 Evaluate side-chains 24 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 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 = 0.3514 r_free = 0.3514 target = 0.097638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.074671 restraints weight = 21025.346| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 5.95 r_work: 0.3003 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.027 2230 Z= 0.351 Angle : 0.621 7.178 3020 Z= 0.345 Chirality : 0.047 0.128 340 Planarity : 0.004 0.010 400 Dihedral : 4.500 9.701 310 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.42 % Allowed : 4.58 % Favored : 95.00 % 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: -4.93 (0.26), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.20), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.004 PHE G 15 TYR 0.005 0.001 TYR A 37 ARG 0.001 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.04969 ( 80) hydrogen bonds : angle 4.85655 ( 232) covalent geometry : bond 0.00769 ( 2220) covalent geometry : angle 0.62142 ( 3020) Misc. bond : bond 0.00142 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.215 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.0675 time to fit residues: 3.0131 Evaluate side-chains 26 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.105141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081129 restraints weight = 16883.737| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 5.86 r_work: 0.3076 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2230 Z= 0.119 Angle : 0.445 7.766 3020 Z= 0.240 Chirality : 0.043 0.127 340 Planarity : 0.002 0.005 400 Dihedral : 3.527 7.387 310 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.42 % Allowed : 8.33 % Favored : 91.25 % 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: -4.95 (0.28), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.21), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE F 15 TYR 0.003 0.000 TYR G 37 ARG 0.000 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.02721 ( 80) hydrogen bonds : angle 4.50734 ( 232) covalent geometry : bond 0.00262 ( 2220) covalent geometry : angle 0.44520 ( 3020) Misc. bond : bond 0.00037 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.200 Fit side-chains REVERT: G 19 SER cc_start: 0.8619 (t) cc_final: 0.8260 (p) REVERT: H 19 SER cc_start: 0.8563 (t) cc_final: 0.8248 (p) REVERT: I 11 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7552 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.0987 time to fit residues: 3.6821 Evaluate side-chains 29 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.110991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.086790 restraints weight = 16760.286| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 5.57 r_work: 0.3102 rms_B_bonded: 5.02 restraints_weight: 2.0000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2230 Z= 0.093 Angle : 0.399 6.709 3020 Z= 0.218 Chirality : 0.042 0.122 340 Planarity : 0.001 0.004 400 Dihedral : 3.304 7.255 310 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.83 % Allowed : 7.50 % Favored : 91.67 % 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: -4.92 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE F 15 TYR 0.006 0.001 TYR G 37 ARG 0.000 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.02248 ( 80) hydrogen bonds : angle 4.28526 ( 232) covalent geometry : bond 0.00201 ( 2220) covalent geometry : angle 0.39883 ( 3020) Misc. bond : bond 0.00032 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.233 Fit side-chains REVERT: G 19 SER cc_start: 0.8527 (t) cc_final: 0.8237 (p) REVERT: H 19 SER cc_start: 0.8465 (t) cc_final: 0.8180 (p) outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.0632 time to fit residues: 2.4355 Evaluate side-chains 28 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 0.1980 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.112679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088536 restraints weight = 16599.310| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 5.59 r_work: 0.3143 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 2230 Z= 0.068 Angle : 0.380 6.275 3020 Z= 0.207 Chirality : 0.042 0.121 340 Planarity : 0.001 0.003 400 Dihedral : 3.116 7.133 310 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.25 % Allowed : 6.67 % Favored : 92.08 % 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: -4.90 (0.31), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE F 15 TYR 0.005 0.000 TYR G 37 ARG 0.000 0.000 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.01800 ( 80) hydrogen bonds : angle 4.15256 ( 232) covalent geometry : bond 0.00145 ( 2220) covalent geometry : angle 0.38045 ( 3020) Misc. bond : bond 0.00017 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.221 Fit side-chains REVERT: G 19 SER cc_start: 0.8504 (t) cc_final: 0.8264 (p) REVERT: H 19 SER cc_start: 0.8411 (t) cc_final: 0.8201 (p) outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.0660 time to fit residues: 2.5251 Evaluate side-chains 28 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 0.8980 overall best weight: 4.5386 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.098456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.075260 restraints weight = 19167.816| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 5.35 r_work: 0.3019 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.028 2230 Z= 0.348 Angle : 0.602 6.317 3020 Z= 0.336 Chirality : 0.046 0.128 340 Planarity : 0.003 0.009 400 Dihedral : 4.210 10.176 310 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 2.08 % Allowed : 7.50 % Favored : 90.42 % 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: -5.22 (0.28), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.21), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.004 PHE G 15 TYR 0.010 0.001 TYR G 37 ARG 0.000 0.000 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 80) hydrogen bonds : angle 4.73008 ( 232) covalent geometry : bond 0.00760 ( 2220) covalent geometry : angle 0.60229 ( 3020) Misc. bond : bond 0.00106 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.216 Fit side-chains REVERT: J 11 ARG cc_start: 0.8324 (mtt180) cc_final: 0.7819 (ttm110) outliers start: 5 outliers final: 5 residues processed: 35 average time/residue: 0.0888 time to fit residues: 4.0782 Evaluate side-chains 33 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN G 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.111741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.086949 restraints weight = 18454.585| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 5.53 r_work: 0.3097 rms_B_bonded: 5.36 restraints_weight: 2.0000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2230 Z= 0.080 Angle : 0.410 6.189 3020 Z= 0.222 Chirality : 0.042 0.121 340 Planarity : 0.001 0.009 400 Dihedral : 3.268 7.107 310 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.83 % Allowed : 12.08 % Favored : 87.08 % 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: -5.03 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE F 15 TYR 0.007 0.001 TYR G 37 ARG 0.001 0.000 ARG I 11 Details of bonding type rmsd hydrogen bonds : bond 0.02053 ( 80) hydrogen bonds : angle 4.55065 ( 232) covalent geometry : bond 0.00168 ( 2220) covalent geometry : angle 0.41013 ( 3020) Misc. bond : bond 0.00021 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.248 Fit side-chains REVERT: G 19 SER cc_start: 0.8541 (t) cc_final: 0.8219 (p) REVERT: H 19 SER cc_start: 0.8576 (t) cc_final: 0.8252 (p) REVERT: I 11 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7636 (mtm-85) REVERT: J 11 ARG cc_start: 0.8287 (mtt180) cc_final: 0.7797 (ttm110) outliers start: 2 outliers final: 2 residues processed: 29 average time/residue: 0.1313 time to fit residues: 4.7218 Evaluate side-chains 28 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.107177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.082997 restraints weight = 16427.958| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 5.24 r_work: 0.3036 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2230 Z= 0.235 Angle : 0.513 6.069 3020 Z= 0.286 Chirality : 0.044 0.127 340 Planarity : 0.002 0.008 400 Dihedral : 3.819 8.843 310 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.38 % Favored : 84.62 % Rotamer: Outliers : 2.08 % Allowed : 10.83 % Favored : 87.08 % 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: -5.13 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE G 15 TYR 0.009 0.001 TYR G 37 ARG 0.000 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 80) hydrogen bonds : angle 4.65546 ( 232) covalent geometry : bond 0.00514 ( 2220) covalent geometry : angle 0.51338 ( 3020) Misc. bond : bond 0.00074 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.216 Fit side-chains REVERT: G 19 SER cc_start: 0.8652 (t) cc_final: 0.8190 (p) REVERT: I 11 ARG cc_start: 0.8014 (mtt180) cc_final: 0.7617 (mtm-85) REVERT: J 11 ARG cc_start: 0.8302 (mtt180) cc_final: 0.7797 (ttm110) outliers start: 5 outliers final: 5 residues processed: 30 average time/residue: 0.1244 time to fit residues: 4.6154 Evaluate side-chains 35 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 0 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.111685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.086755 restraints weight = 20420.282| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 5.70 r_work: 0.3079 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2230 Z= 0.089 Angle : 0.411 6.063 3020 Z= 0.225 Chirality : 0.043 0.123 340 Planarity : 0.002 0.008 400 Dihedral : 3.303 7.093 310 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.67 % Allowed : 11.67 % Favored : 86.67 % 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: -4.97 (0.31), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.24), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE H 15 TYR 0.009 0.001 TYR F 37 ARG 0.000 0.000 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.02111 ( 80) hydrogen bonds : angle 4.56011 ( 232) covalent geometry : bond 0.00197 ( 2220) covalent geometry : angle 0.41123 ( 3020) Misc. bond : bond 0.00023 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.225 Fit side-chains REVERT: G 19 SER cc_start: 0.8575 (t) cc_final: 0.8214 (p) REVERT: H 19 SER cc_start: 0.8562 (t) cc_final: 0.8219 (p) REVERT: I 11 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7603 (mtm-85) REVERT: J 11 ARG cc_start: 0.8297 (mtt180) cc_final: 0.7771 (ttm110) outliers start: 4 outliers final: 4 residues processed: 31 average time/residue: 0.1307 time to fit residues: 5.0433 Evaluate side-chains 33 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.111457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.086567 restraints weight = 19078.395| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 5.55 r_work: 0.3079 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2230 Z= 0.113 Angle : 0.419 5.849 3020 Z= 0.231 Chirality : 0.042 0.123 340 Planarity : 0.002 0.008 400 Dihedral : 3.336 7.291 310 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.67 % Allowed : 11.67 % Favored : 86.67 % 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: -4.95 (0.32), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.24), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE F 15 TYR 0.009 0.001 TYR F 37 ARG 0.000 0.000 ARG E 11 Details of bonding type rmsd hydrogen bonds : bond 0.02467 ( 80) hydrogen bonds : angle 4.43635 ( 232) covalent geometry : bond 0.00247 ( 2220) covalent geometry : angle 0.41901 ( 3020) Misc. bond : bond 0.00033 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1558.56 seconds wall clock time: 27 minutes 33.26 seconds (1653.26 seconds total)