Starting phenix.real_space_refine on Wed Jun 4 17:17:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5p_37300/06_2025/8w5p_37300.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5p_37300/06_2025/8w5p_37300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5p_37300/06_2025/8w5p_37300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5p_37300/06_2025/8w5p_37300.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5p_37300/06_2025/8w5p_37300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5p_37300/06_2025/8w5p_37300.cif" } resolution = 3.3 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= 0.010 sd= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 2251 2.51 5 N 606 2.21 5 O 714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3582 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 873 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "C" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 935 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain breaks: 1 Chain: "c" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 956 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain breaks: 1 Time building chain proxies: 2.84, per 1000 atoms: 0.79 Number of scatterers: 3582 At special positions: 0 Unit cell: (97.68, 63.36, 80.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 714 8.00 N 606 7.00 C 2251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 437.4 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 876 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 5 sheets defined 10.8% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'C' and resid 101 through 116 removed outlier: 3.751A pdb=" N ARG C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'c' and resid 41 through 45 removed outlier: 4.261A pdb=" N GLU c 45 " --> pdb=" O PRO c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 101 through 116 Processing helix chain 'c' and resid 118 through 125 removed outlier: 3.538A pdb=" N ASP c 123 " --> pdb=" O PRO c 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 7 through 9 removed outlier: 3.620A pdb=" N THR L 72 " --> pdb=" O THR L 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 62 through 63 removed outlier: 6.527A pdb=" N TRP L 44 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR L 58 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU L 42 " --> pdb=" O TYR L 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.641A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 97 through 102 removed outlier: 7.473A pdb=" N TYR H 97 " --> pdb=" O GLN H 113 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLN H 113 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N CYS H 99 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TRP H 111 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR H 101 " --> pdb=" O ASP H 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 11 removed outlier: 6.001A pdb=" N GLN C 17 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER C 34 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL C 26 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG C 86 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL c 84 " --> pdb=" O CYS c 74 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS c 74 " --> pdb=" O VAL c 84 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG c 86 " --> pdb=" O THR c 72 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N SER c 34 " --> pdb=" O ARG c 24 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN c 17 " --> pdb=" O ASN c 10 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN c 10 " --> pdb=" O GLN c 17 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 321 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: 0.76 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 601 1.30 - 1.42: 925 1.42 - 1.55: 2111 1.55 - 1.68: 1 1.68 - 1.81: 14 Bond restraints: 3652 Sorted by residual: bond pdb=" C TRP H 50 " pdb=" O TRP H 50 " ideal model delta sigma weight residual 1.234 1.168 0.066 1.24e-02 6.50e+03 2.83e+01 bond pdb=" C GLU H 49 " pdb=" O GLU H 49 " ideal model delta sigma weight residual 1.235 1.168 0.068 1.28e-02 6.10e+03 2.79e+01 bond pdb=" C ILE H 51 " pdb=" O ILE H 51 " ideal model delta sigma weight residual 1.235 1.182 0.053 1.45e-02 4.76e+03 1.35e+01 bond pdb=" CB TRP H 50 " pdb=" CG TRP H 50 " ideal model delta sigma weight residual 1.498 1.387 0.111 3.10e-02 1.04e+03 1.29e+01 bond pdb=" C LEU H 48 " pdb=" O LEU H 48 " ideal model delta sigma weight residual 1.234 1.192 0.043 1.22e-02 6.72e+03 1.21e+01 ... (remaining 3647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 4793 1.82 - 3.64: 146 3.64 - 5.46: 24 5.46 - 7.27: 5 7.27 - 9.09: 1 Bond angle restraints: 4969 Sorted by residual: angle pdb=" N TRP H 50 " pdb=" CA TRP H 50 " pdb=" CB TRP H 50 " ideal model delta sigma weight residual 110.04 103.78 6.26 1.47e+00 4.63e-01 1.81e+01 angle pdb=" N TRP H 50 " pdb=" CA TRP H 50 " pdb=" C TRP H 50 " ideal model delta sigma weight residual 110.35 115.13 -4.78 1.36e+00 5.41e-01 1.23e+01 angle pdb=" C GLU H 46 " pdb=" N SER H 47 " pdb=" CA SER H 47 " ideal model delta sigma weight residual 121.54 128.12 -6.58 1.91e+00 2.74e-01 1.19e+01 angle pdb=" N SER H 47 " pdb=" CA SER H 47 " pdb=" C SER H 47 " ideal model delta sigma weight residual 110.80 117.84 -7.04 2.13e+00 2.20e-01 1.09e+01 angle pdb=" N GLU H 49 " pdb=" CA GLU H 49 " pdb=" C GLU H 49 " ideal model delta sigma weight residual 109.40 114.75 -5.35 1.63e+00 3.76e-01 1.08e+01 ... (remaining 4964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 1956 15.93 - 31.85: 177 31.85 - 47.78: 38 47.78 - 63.71: 9 63.71 - 79.63: 4 Dihedral angle restraints: 2184 sinusoidal: 821 harmonic: 1363 Sorted by residual: dihedral pdb=" CA GLN L 98 " pdb=" C GLN L 98 " pdb=" N GLN L 99 " pdb=" CA GLN L 99 " ideal model delta harmonic sigma weight residual 180.00 164.14 15.86 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA GLU H 49 " pdb=" CB GLU H 49 " pdb=" CG GLU H 49 " pdb=" CD GLU H 49 " ideal model delta sinusoidal sigma weight residual -180.00 -120.87 -59.13 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYS C 16 " pdb=" CD LYS C 16 " pdb=" CE LYS C 16 " pdb=" NZ LYS C 16 " ideal model delta sinusoidal sigma weight residual -180.00 -127.17 -52.83 3 1.50e+01 4.44e-03 9.15e+00 ... (remaining 2181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 487 0.063 - 0.127: 79 0.127 - 0.190: 6 0.190 - 0.253: 1 0.253 - 0.317: 1 Chirality restraints: 574 Sorted by residual: chirality pdb=" CA SER H 47 " pdb=" N SER H 47 " pdb=" C SER H 47 " pdb=" CB SER H 47 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB THR c 93 " pdb=" CA THR c 93 " pdb=" OG1 THR c 93 " pdb=" CG2 THR c 93 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB THR L 83 " pdb=" CA THR L 83 " pdb=" OG1 THR L 83 " pdb=" CG2 THR L 83 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.49e-01 ... (remaining 571 not shown) Planarity restraints: 641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU H 46 " 0.025 2.00e-02 2.50e+03 5.40e-02 2.92e+01 pdb=" C GLU H 46 " -0.093 2.00e-02 2.50e+03 pdb=" O GLU H 46 " 0.036 2.00e-02 2.50e+03 pdb=" N SER H 47 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 49 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C GLU H 49 " 0.046 2.00e-02 2.50e+03 pdb=" O GLU H 49 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP H 50 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY H 11 " -0.037 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO H 12 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO H 12 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 12 " -0.032 5.00e-02 4.00e+02 ... (remaining 638 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 282 2.74 - 3.28: 3547 3.28 - 3.82: 5389 3.82 - 4.36: 6233 4.36 - 4.90: 11203 Nonbonded interactions: 26654 Sorted by model distance: nonbonded pdb=" O LEU c 8 " pdb=" OG1 THR c 18 " model vdw 2.196 3.040 nonbonded pdb=" O SER H 47 " pdb=" OG SER H 47 " model vdw 2.288 3.040 nonbonded pdb=" OG SER L 76 " pdb=" O ASP L 79 " model vdw 2.304 3.040 nonbonded pdb=" OG SER L 35 " pdb=" O ASN L 37 " model vdw 2.316 3.040 nonbonded pdb=" O SER C 95 " pdb=" OG SER C 95 " model vdw 2.319 3.040 ... (remaining 26649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'c' and (resid 1 through 55 or resid 61 through 131)) } 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.150 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.006 0.111 3653 Z= 0.295 Angle : 0.739 9.092 4971 Z= 0.415 Chirality : 0.047 0.317 574 Planarity : 0.006 0.057 641 Dihedral : 13.584 79.633 1305 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.94 % Favored : 92.84 % Rotamer: Outliers : 0.50 % Allowed : 0.76 % Favored : 98.74 % 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: -2.56 (0.36), residues: 461 helix: -0.75 (0.74), residues: 47 sheet: -1.05 (0.40), residues: 177 loop : -2.45 (0.34), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP H 111 HIS 0.005 0.001 HIS H 38 PHE 0.009 0.001 PHE L 80 TYR 0.013 0.001 TYR L 100 ARG 0.009 0.001 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.20598 ( 120) hydrogen bonds : angle 8.05504 ( 321) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.13353 ( 2) covalent geometry : bond 0.00556 ( 3652) covalent geometry : angle 0.73964 ( 4969) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.471 Fit side-chains REVERT: c 2 LYS cc_start: 0.8156 (tttp) cc_final: 0.7924 (tttp) REVERT: c 53 SER cc_start: 0.8211 (t) cc_final: 0.7995 (t) outliers start: 2 outliers final: 2 residues processed: 109 average time/residue: 0.1682 time to fit residues: 22.1344 Evaluate side-chains 100 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 48 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.122407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.086988 restraints weight = 4752.709| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.06 r_work: 0.3004 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3653 Z= 0.234 Angle : 0.693 7.163 4971 Z= 0.366 Chirality : 0.047 0.149 574 Planarity : 0.005 0.052 641 Dihedral : 5.221 38.504 506 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.68 % Favored : 91.11 % Rotamer: Outliers : 1.76 % Allowed : 12.59 % Favored : 85.64 % 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: -2.72 (0.36), residues: 461 helix: -1.11 (0.72), residues: 48 sheet: -1.22 (0.38), residues: 185 loop : -2.47 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 111 HIS 0.005 0.001 HIS H 38 PHE 0.014 0.002 PHE C 94 TYR 0.013 0.002 TYR L 58 ARG 0.004 0.001 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 120) hydrogen bonds : angle 6.20244 ( 321) SS BOND : bond 0.00307 ( 1) SS BOND : angle 0.10134 ( 2) covalent geometry : bond 0.00552 ( 3652) covalent geometry : angle 0.69294 ( 4969) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.398 Fit side-chains REVERT: L 90 GLU cc_start: 0.7554 (tp30) cc_final: 0.7281 (tp30) REVERT: H 14 LEU cc_start: 0.7586 (tp) cc_final: 0.7321 (tp) REVERT: H 26 LYS cc_start: 0.7510 (tptt) cc_final: 0.7238 (tppt) REVERT: H 49 GLU cc_start: 0.8226 (pm20) cc_final: 0.7689 (pm20) REVERT: c 53 SER cc_start: 0.8383 (t) cc_final: 0.8140 (t) outliers start: 7 outliers final: 6 residues processed: 106 average time/residue: 0.1689 time to fit residues: 21.5858 Evaluate side-chains 106 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain c residue 122 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.089806 restraints weight = 4554.112| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.05 r_work: 0.3003 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3653 Z= 0.163 Angle : 0.642 6.923 4971 Z= 0.336 Chirality : 0.045 0.136 574 Planarity : 0.004 0.047 641 Dihedral : 4.652 20.525 501 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.38 % Favored : 92.41 % Rotamer: Outliers : 3.02 % Allowed : 18.39 % Favored : 78.59 % 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: -2.65 (0.36), residues: 461 helix: -1.03 (0.73), residues: 48 sheet: -1.17 (0.38), residues: 185 loop : -2.43 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 111 HIS 0.005 0.001 HIS H 38 PHE 0.011 0.001 PHE C 94 TYR 0.010 0.001 TYR L 58 ARG 0.005 0.001 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 120) hydrogen bonds : angle 5.72644 ( 321) SS BOND : bond 0.00343 ( 1) SS BOND : angle 0.05625 ( 2) covalent geometry : bond 0.00384 ( 3652) covalent geometry : angle 0.64185 ( 4969) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.434 Fit side-chains REVERT: L 51 GLN cc_start: 0.8560 (pm20) cc_final: 0.7910 (pm20) REVERT: L 90 GLU cc_start: 0.7694 (tp30) cc_final: 0.7445 (tp30) REVERT: H 14 LEU cc_start: 0.7521 (tp) cc_final: 0.7211 (tp) REVERT: H 49 GLU cc_start: 0.8095 (pm20) cc_final: 0.7452 (pm20) REVERT: C 21 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7817 (pp) REVERT: c 53 SER cc_start: 0.8109 (t) cc_final: 0.7822 (t) outliers start: 12 outliers final: 9 residues processed: 111 average time/residue: 0.1678 time to fit residues: 22.4310 Evaluate side-chains 113 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 118 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 38 optimal weight: 0.0970 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 46 GLN L 51 GLN c 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.129430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.093033 restraints weight = 4470.837| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.08 r_work: 0.3063 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3653 Z= 0.104 Angle : 0.596 6.929 4971 Z= 0.308 Chirality : 0.043 0.131 574 Planarity : 0.004 0.043 641 Dihedral : 4.268 19.352 501 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.38 % Favored : 92.41 % Rotamer: Outliers : 3.78 % Allowed : 19.40 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.36), residues: 461 helix: -0.67 (0.75), residues: 49 sheet: -0.98 (0.38), residues: 185 loop : -2.38 (0.35), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 59 HIS 0.005 0.001 HIS H 38 PHE 0.008 0.001 PHE L 106 TYR 0.006 0.001 TYR L 58 ARG 0.005 0.000 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 120) hydrogen bonds : angle 5.26829 ( 321) SS BOND : bond 0.00375 ( 1) SS BOND : angle 0.21893 ( 2) covalent geometry : bond 0.00238 ( 3652) covalent geometry : angle 0.59586 ( 4969) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.411 Fit side-chains REVERT: L 51 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: H 49 GLU cc_start: 0.7925 (pm20) cc_final: 0.7304 (pm20) REVERT: c 21 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7620 (pp) REVERT: c 53 SER cc_start: 0.8147 (t) cc_final: 0.7912 (t) outliers start: 15 outliers final: 9 residues processed: 112 average time/residue: 0.1562 time to fit residues: 21.4771 Evaluate side-chains 105 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 46 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.088725 restraints weight = 4659.239| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.08 r_work: 0.2984 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3653 Z= 0.205 Angle : 0.643 6.672 4971 Z= 0.339 Chirality : 0.046 0.139 574 Planarity : 0.004 0.044 641 Dihedral : 4.588 19.656 501 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.89 % Favored : 90.89 % Rotamer: Outliers : 6.30 % Allowed : 19.14 % Favored : 74.56 % 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: -2.58 (0.37), residues: 461 helix: -0.99 (0.73), residues: 49 sheet: -1.16 (0.37), residues: 202 loop : -2.40 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 59 HIS 0.005 0.001 HIS H 38 PHE 0.008 0.001 PHE L 106 TYR 0.013 0.001 TYR L 58 ARG 0.004 0.000 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 120) hydrogen bonds : angle 5.31521 ( 321) SS BOND : bond 0.00280 ( 1) SS BOND : angle 0.15208 ( 2) covalent geometry : bond 0.00496 ( 3652) covalent geometry : angle 0.64277 ( 4969) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.347 Fit side-chains REVERT: H 26 LYS cc_start: 0.7163 (tppt) cc_final: 0.6951 (tptt) REVERT: H 70 LYS cc_start: 0.7151 (ptpp) cc_final: 0.6734 (ptpt) REVERT: H 76 ASP cc_start: 0.7274 (t0) cc_final: 0.7062 (t0) REVERT: H 83 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.7082 (p90) REVERT: c 18 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8657 (t) REVERT: c 53 SER cc_start: 0.8235 (t) cc_final: 0.7948 (t) REVERT: c 60 LYS cc_start: 0.7276 (tptt) cc_final: 0.6616 (tppt) REVERT: c 93 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8029 (p) REVERT: c 127 GLN cc_start: 0.9040 (mp10) cc_final: 0.8656 (mp10) outliers start: 25 outliers final: 18 residues processed: 116 average time/residue: 0.1685 time to fit residues: 23.7446 Evaluate side-chains 120 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 36 SER Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 93 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.0470 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 26 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.129661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.092968 restraints weight = 4577.379| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.11 r_work: 0.3059 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3653 Z= 0.106 Angle : 0.596 6.371 4971 Z= 0.307 Chirality : 0.043 0.132 574 Planarity : 0.004 0.041 641 Dihedral : 4.247 18.796 501 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.59 % Favored : 92.19 % Rotamer: Outliers : 4.28 % Allowed : 21.41 % Favored : 74.31 % 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: -2.24 (0.37), residues: 461 helix: -0.56 (0.74), residues: 49 sheet: -0.79 (0.38), residues: 192 loop : -2.36 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.004 0.001 HIS H 38 PHE 0.006 0.001 PHE L 80 TYR 0.006 0.001 TYR L 58 ARG 0.007 0.000 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 120) hydrogen bonds : angle 5.02021 ( 321) SS BOND : bond 0.00326 ( 1) SS BOND : angle 0.15214 ( 2) covalent geometry : bond 0.00257 ( 3652) covalent geometry : angle 0.59628 ( 4969) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.408 Fit side-chains REVERT: L 51 GLN cc_start: 0.8758 (pm20) cc_final: 0.8297 (pm20) REVERT: H 49 GLU cc_start: 0.8036 (pm20) cc_final: 0.7561 (pm20) REVERT: H 76 ASP cc_start: 0.7109 (t0) cc_final: 0.6780 (t0) REVERT: H 83 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6749 (p90) REVERT: c 53 SER cc_start: 0.8127 (t) cc_final: 0.7877 (t) REVERT: c 60 LYS cc_start: 0.7302 (tptt) cc_final: 0.6702 (tppt) REVERT: c 93 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7859 (p) REVERT: c 127 GLN cc_start: 0.8930 (mp10) cc_final: 0.8648 (mp10) outliers start: 17 outliers final: 13 residues processed: 106 average time/residue: 0.1567 time to fit residues: 20.3326 Evaluate side-chains 108 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 93 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.0030 chunk 30 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 0.0370 overall best weight: 0.4868 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.130636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.094408 restraints weight = 4595.248| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.11 r_work: 0.3094 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 3653 Z= 0.100 Angle : 0.584 6.145 4971 Z= 0.299 Chirality : 0.043 0.144 574 Planarity : 0.004 0.039 641 Dihedral : 4.055 18.257 501 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.38 % Favored : 92.41 % Rotamer: Outliers : 4.79 % Allowed : 22.17 % Favored : 73.05 % 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: -1.98 (0.37), residues: 461 helix: -0.13 (0.75), residues: 49 sheet: -0.62 (0.37), residues: 193 loop : -2.26 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 PHE 0.006 0.001 PHE L 80 TYR 0.009 0.001 TYR H 83 ARG 0.006 0.000 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.02838 ( 120) hydrogen bonds : angle 4.74431 ( 321) SS BOND : bond 0.00333 ( 1) SS BOND : angle 0.29136 ( 2) covalent geometry : bond 0.00246 ( 3652) covalent geometry : angle 0.58371 ( 4969) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.418 Fit side-chains REVERT: L 51 GLN cc_start: 0.8652 (pm20) cc_final: 0.8160 (pm20) REVERT: L 90 GLU cc_start: 0.8102 (tp30) cc_final: 0.7878 (tm-30) REVERT: H 76 ASP cc_start: 0.7134 (t0) cc_final: 0.6758 (t0) REVERT: H 83 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.6538 (p90) REVERT: c 18 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8374 (t) REVERT: c 53 SER cc_start: 0.8135 (t) cc_final: 0.7906 (t) REVERT: c 60 LYS cc_start: 0.7233 (tptt) cc_final: 0.6740 (tppt) REVERT: c 93 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7843 (p) outliers start: 19 outliers final: 13 residues processed: 109 average time/residue: 0.1553 time to fit residues: 20.6850 Evaluate side-chains 111 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 36 SER Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 93 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 34 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 30 GLN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089187 restraints weight = 4625.793| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.01 r_work: 0.2999 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3653 Z= 0.220 Angle : 0.663 6.541 4971 Z= 0.347 Chirality : 0.046 0.140 574 Planarity : 0.004 0.042 641 Dihedral : 4.663 19.584 501 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.03 % Favored : 91.76 % Rotamer: Outliers : 6.05 % Allowed : 21.41 % Favored : 72.54 % 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: -2.26 (0.37), residues: 461 helix: -0.72 (0.74), residues: 49 sheet: -0.96 (0.37), residues: 200 loop : -2.18 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 50 HIS 0.004 0.001 HIS H 38 PHE 0.008 0.001 PHE L 101 TYR 0.012 0.002 TYR L 58 ARG 0.005 0.001 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 120) hydrogen bonds : angle 5.14666 ( 321) SS BOND : bond 0.00461 ( 1) SS BOND : angle 0.08423 ( 2) covalent geometry : bond 0.00527 ( 3652) covalent geometry : angle 0.66279 ( 4969) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.383 Fit side-chains REVERT: L 51 GLN cc_start: 0.8603 (pm20) cc_final: 0.8087 (pm20) REVERT: H 76 ASP cc_start: 0.7312 (t0) cc_final: 0.7048 (t0) REVERT: c 18 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8696 (t) REVERT: c 53 SER cc_start: 0.8259 (t) cc_final: 0.7963 (t) REVERT: c 60 LYS cc_start: 0.7176 (tptt) cc_final: 0.6429 (tppt) REVERT: c 93 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7846 (p) outliers start: 24 outliers final: 17 residues processed: 116 average time/residue: 0.1638 time to fit residues: 23.0115 Evaluate side-chains 115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 36 SER Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 93 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 9.9990 chunk 23 optimal weight: 0.0040 chunk 1 optimal weight: 0.5980 chunk 44 optimal weight: 0.0370 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 0.0370 chunk 30 optimal weight: 0.9990 overall best weight: 0.2748 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.130713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094595 restraints weight = 4511.036| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.11 r_work: 0.3080 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 3653 Z= 0.117 Angle : 0.629 6.756 4971 Z= 0.324 Chirality : 0.043 0.150 574 Planarity : 0.004 0.040 641 Dihedral : 4.198 17.806 501 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.28 % Allowed : 23.43 % Favored : 72.29 % 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: -2.01 (0.37), residues: 461 helix: -0.26 (0.75), residues: 49 sheet: -0.66 (0.38), residues: 191 loop : -2.20 (0.36), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 50 HIS 0.004 0.001 HIS H 38 PHE 0.008 0.001 PHE L 80 TYR 0.018 0.001 TYR H 30 ARG 0.008 0.001 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.02822 ( 120) hydrogen bonds : angle 4.69785 ( 321) SS BOND : bond 0.00383 ( 1) SS BOND : angle 0.24463 ( 2) covalent geometry : bond 0.00319 ( 3652) covalent geometry : angle 0.62894 ( 4969) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.403 Fit side-chains REVERT: L 51 GLN cc_start: 0.8645 (pm20) cc_final: 0.8163 (pm20) REVERT: H 76 ASP cc_start: 0.7017 (t0) cc_final: 0.6690 (t0) REVERT: H 97 TYR cc_start: 0.8435 (m-10) cc_final: 0.8108 (m-10) REVERT: c 4 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8254 (mt-10) REVERT: c 53 SER cc_start: 0.8101 (t) cc_final: 0.7832 (t) REVERT: c 60 LYS cc_start: 0.7256 (tptt) cc_final: 0.6738 (tppt) REVERT: c 87 GLN cc_start: 0.8297 (mm110) cc_final: 0.8041 (mm110) REVERT: c 93 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7846 (p) outliers start: 17 outliers final: 14 residues processed: 107 average time/residue: 0.1420 time to fit residues: 18.7956 Evaluate side-chains 108 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 36 SER Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 30 GLN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.092225 restraints weight = 4577.616| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.08 r_work: 0.3051 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 3653 Z= 0.138 Angle : 0.644 7.380 4971 Z= 0.332 Chirality : 0.044 0.129 574 Planarity : 0.004 0.039 641 Dihedral : 4.330 19.043 501 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.53 % Allowed : 23.68 % Favored : 71.79 % 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: -1.99 (0.38), residues: 461 helix: -0.28 (0.74), residues: 49 sheet: -0.75 (0.37), residues: 200 loop : -2.12 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 50 HIS 0.004 0.001 HIS H 38 PHE 0.006 0.001 PHE L 80 TYR 0.019 0.001 TYR H 30 ARG 0.008 0.001 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.02969 ( 120) hydrogen bonds : angle 4.72745 ( 321) SS BOND : bond 0.00309 ( 1) SS BOND : angle 0.16039 ( 2) covalent geometry : bond 0.00362 ( 3652) covalent geometry : angle 0.64424 ( 4969) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.378 Fit side-chains REVERT: L 51 GLN cc_start: 0.8752 (pm20) cc_final: 0.8229 (pm20) REVERT: H 76 ASP cc_start: 0.7062 (t0) cc_final: 0.6844 (t0) REVERT: c 4 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8278 (mt-10) REVERT: c 18 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8454 (t) REVERT: c 53 SER cc_start: 0.8207 (t) cc_final: 0.7910 (t) REVERT: c 60 LYS cc_start: 0.7126 (tptt) cc_final: 0.6627 (tppt) REVERT: c 87 GLN cc_start: 0.8401 (mm110) cc_final: 0.8170 (mm110) REVERT: c 93 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7847 (p) outliers start: 18 outliers final: 15 residues processed: 105 average time/residue: 0.1514 time to fit residues: 19.5540 Evaluate side-chains 110 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 36 SER Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 14 optimal weight: 0.0970 chunk 6 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 30 GLN L 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.093473 restraints weight = 4589.905| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.09 r_work: 0.3069 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 3653 Z= 0.123 Angle : 0.640 7.580 4971 Z= 0.329 Chirality : 0.043 0.125 574 Planarity : 0.004 0.038 641 Dihedral : 4.270 18.856 501 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.79 % Allowed : 23.68 % Favored : 71.54 % 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: -1.92 (0.38), residues: 461 helix: -0.16 (0.74), residues: 49 sheet: -0.70 (0.38), residues: 200 loop : -2.10 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 50 HIS 0.004 0.001 HIS H 38 PHE 0.006 0.001 PHE c 94 TYR 0.019 0.001 TYR H 30 ARG 0.008 0.001 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 120) hydrogen bonds : angle 4.63116 ( 321) SS BOND : bond 0.00338 ( 1) SS BOND : angle 0.15116 ( 2) covalent geometry : bond 0.00330 ( 3652) covalent geometry : angle 0.64033 ( 4969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2137.94 seconds wall clock time: 37 minutes 33.11 seconds (2253.11 seconds total)