Starting phenix.real_space_refine on Tue Jan 14 07:25:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk9_19265/01_2025/8rk9_19265.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk9_19265/01_2025/8rk9_19265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rk9_19265/01_2025/8rk9_19265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk9_19265/01_2025/8rk9_19265.map" model { file = "/net/cci-nas-00/data/ceres_data/8rk9_19265/01_2025/8rk9_19265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk9_19265/01_2025/8rk9_19265.cif" } resolution = 3.95 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= 0.000 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 3912 2.51 5 N 1074 2.21 5 O 1152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6138 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1023 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 10, 'TRANS': 125} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 3.33, per 1000 atoms: 0.54 Number of scatterers: 6138 At special positions: 0 Unit cell: (95.864, 95.864, 57.5184, 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 1152 8.00 N 1074 7.00 C 3912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 1.4 seconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 12 sheets defined 19.9% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 removed outlier: 5.028A pdb=" N ARG A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.754A pdb=" N ALA A 68 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE A 69 " --> pdb=" O GLN A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 97 through 109 removed outlier: 3.881A pdb=" N LEU A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 removed outlier: 5.027A pdb=" N ARG B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.754A pdb=" N ALA B 68 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE B 69 " --> pdb=" O GLN B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 69' Processing helix chain 'B' and resid 97 through 109 removed outlier: 3.881A pdb=" N LEU B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 19 removed outlier: 5.028A pdb=" N ARG C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 69 removed outlier: 3.754A pdb=" N ALA C 68 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE C 69 " --> pdb=" O GLN C 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 69' Processing helix chain 'C' and resid 97 through 109 removed outlier: 3.881A pdb=" N LEU C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 19 removed outlier: 5.028A pdb=" N ARG D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.754A pdb=" N ALA D 68 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE D 69 " --> pdb=" O GLN D 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 69' Processing helix chain 'D' and resid 97 through 109 removed outlier: 3.881A pdb=" N LEU D 101 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 19 removed outlier: 5.028A pdb=" N ARG E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 69 removed outlier: 3.754A pdb=" N ALA E 68 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE E 69 " --> pdb=" O GLN E 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 65 through 69' Processing helix chain 'E' and resid 97 through 109 removed outlier: 3.881A pdb=" N LEU E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 19 removed outlier: 5.028A pdb=" N ARG F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 69 removed outlier: 3.754A pdb=" N ALA F 68 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE F 69 " --> pdb=" O GLN F 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 65 through 69' Processing helix chain 'F' and resid 97 through 109 removed outlier: 3.881A pdb=" N LEU F 101 " --> pdb=" O GLU F 97 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=2, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=3, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=4, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=5, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=6, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=7, first strand: chain 'D' and resid 49 through 50 Processing sheet with id=8, first strand: chain 'D' and resid 49 through 50 Processing sheet with id=9, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=10, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=11, first strand: chain 'F' and resid 49 through 50 Processing sheet with id=12, first strand: chain 'F' and resid 49 through 50 120 hydrogen bonds defined for protein. 324 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: 1.37 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1014 1.29 - 1.36: 1056 1.36 - 1.42: 588 1.42 - 1.48: 984 1.48 - 1.55: 2640 Bond restraints: 6282 Sorted by residual: bond pdb=" CA VAL A 22 " pdb=" CB VAL A 22 " ideal model delta sigma weight residual 1.537 1.540 -0.003 5.00e-03 4.00e+04 4.72e-01 bond pdb=" CA VAL D 22 " pdb=" CB VAL D 22 " ideal model delta sigma weight residual 1.537 1.540 -0.003 5.00e-03 4.00e+04 4.72e-01 bond pdb=" CA VAL E 22 " pdb=" CB VAL E 22 " ideal model delta sigma weight residual 1.537 1.540 -0.003 5.00e-03 4.00e+04 4.56e-01 bond pdb=" CA VAL B 22 " pdb=" CB VAL B 22 " ideal model delta sigma weight residual 1.537 1.540 -0.003 5.00e-03 4.00e+04 4.56e-01 bond pdb=" CA ARG F 67 " pdb=" CB ARG F 67 " ideal model delta sigma weight residual 1.530 1.542 -0.011 1.69e-02 3.50e+03 4.53e-01 ... (remaining 6277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 8356 1.76 - 3.53: 188 3.53 - 5.29: 24 5.29 - 7.06: 0 7.06 - 8.82: 12 Bond angle restraints: 8580 Sorted by residual: angle pdb=" C GLN C 66 " pdb=" N ARG C 67 " pdb=" CA ARG C 67 " ideal model delta sigma weight residual 121.54 126.66 -5.12 1.91e+00 2.74e-01 7.19e+00 angle pdb=" C GLN E 66 " pdb=" N ARG E 67 " pdb=" CA ARG E 67 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" C GLN B 66 " pdb=" N ARG B 67 " pdb=" CA ARG B 67 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" C GLN A 66 " pdb=" N ARG A 67 " pdb=" CA ARG A 67 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.15e+00 angle pdb=" C GLN D 66 " pdb=" N ARG D 67 " pdb=" CA ARG D 67 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.15e+00 ... (remaining 8575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 3343 16.74 - 33.49: 245 33.49 - 50.23: 72 50.23 - 66.97: 18 66.97 - 83.72: 18 Dihedral angle restraints: 3696 sinusoidal: 1392 harmonic: 2304 Sorted by residual: dihedral pdb=" CA ARG D 123 " pdb=" CB ARG D 123 " pdb=" CG ARG D 123 " pdb=" CD ARG D 123 " ideal model delta sinusoidal sigma weight residual -60.00 -104.55 44.55 3 1.50e+01 4.44e-03 8.01e+00 dihedral pdb=" CA ARG A 123 " pdb=" CB ARG A 123 " pdb=" CG ARG A 123 " pdb=" CD ARG A 123 " ideal model delta sinusoidal sigma weight residual -60.00 -104.55 44.55 3 1.50e+01 4.44e-03 8.01e+00 dihedral pdb=" CA ARG B 123 " pdb=" CB ARG B 123 " pdb=" CG ARG B 123 " pdb=" CD ARG B 123 " ideal model delta sinusoidal sigma weight residual -60.00 -104.53 44.53 3 1.50e+01 4.44e-03 8.01e+00 ... (remaining 3693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 504 0.025 - 0.050: 242 0.050 - 0.075: 95 0.075 - 0.100: 63 0.100 - 0.125: 62 Chirality restraints: 966 Sorted by residual: chirality pdb=" CA ILE E 69 " pdb=" N ILE E 69 " pdb=" C ILE E 69 " pdb=" CB ILE E 69 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE F 69 " pdb=" N ILE F 69 " pdb=" C ILE F 69 " pdb=" CB ILE F 69 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA ILE A 69 " pdb=" N ILE A 69 " pdb=" C ILE A 69 " pdb=" CB ILE A 69 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 963 not shown) Planarity restraints: 1128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 66 " -0.005 2.00e-02 2.50e+03 9.17e-03 8.41e-01 pdb=" C GLN F 66 " 0.016 2.00e-02 2.50e+03 pdb=" O GLN F 66 " -0.006 2.00e-02 2.50e+03 pdb=" N ARG F 67 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 66 " 0.005 2.00e-02 2.50e+03 9.11e-03 8.31e-01 pdb=" C GLN D 66 " -0.016 2.00e-02 2.50e+03 pdb=" O GLN D 66 " 0.006 2.00e-02 2.50e+03 pdb=" N ARG D 67 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 66 " -0.005 2.00e-02 2.50e+03 9.11e-03 8.31e-01 pdb=" C GLN A 66 " 0.016 2.00e-02 2.50e+03 pdb=" O GLN A 66 " -0.006 2.00e-02 2.50e+03 pdb=" N ARG A 67 " -0.005 2.00e-02 2.50e+03 ... (remaining 1125 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1868 2.81 - 3.34: 5941 3.34 - 3.86: 9577 3.86 - 4.38: 10559 4.38 - 4.90: 17722 Nonbonded interactions: 45667 Sorted by model distance: nonbonded pdb=" OH TYR B 51 " pdb=" OE1 GLN B 74 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR C 51 " pdb=" OE1 GLN C 74 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 51 " pdb=" OE1 GLN A 74 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR D 51 " pdb=" OE1 GLN D 74 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR E 51 " pdb=" OE1 GLN E 74 " model vdw 2.294 3.040 ... (remaining 45662 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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 group one per residue 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: 26.690 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 16.010 Find NCS groups from input model: 0.130 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0031 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 : 0.002 0.017 6282 Z= 0.145 Angle : 0.670 8.821 8580 Z= 0.324 Chirality : 0.046 0.125 966 Planarity : 0.003 0.016 1128 Dihedral : 15.379 83.718 2232 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % 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: -3.79 (0.28), residues: 792 helix: -1.04 (0.59), residues: 96 sheet: -2.07 (0.42), residues: 156 loop : -3.16 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 76 HIS 0.001 0.000 HIS C 62 PHE 0.004 0.001 PHE C 9 TYR 0.007 0.001 TYR B 138 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2869 time to fit residues: 36.0716 Evaluate side-chains 34 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS C 62 HIS D 62 HIS ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS F 62 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5390 r_free = 0.5390 target = 0.315055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5306 r_free = 0.5306 target = 0.306501 restraints weight = 22540.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5316 r_free = 0.5316 target = 0.307826 restraints weight = 17388.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5326 r_free = 0.5326 target = 0.308986 restraints weight = 14046.710| |-----------------------------------------------------------------------------| r_work (final): 0.5328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0571 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6282 Z= 0.243 Angle : 0.826 8.273 8580 Z= 0.395 Chirality : 0.052 0.128 966 Planarity : 0.008 0.063 1128 Dihedral : 4.432 14.429 894 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 1.28 % Allowed : 11.38 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.27), residues: 792 helix: -1.17 (0.55), residues: 96 sheet: -1.89 (0.43), residues: 144 loop : -3.24 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP F 76 HIS 0.002 0.001 HIS D 62 PHE 0.018 0.002 PHE F 147 TYR 0.013 0.001 TYR D 51 ARG 0.008 0.001 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 30 average time/residue: 0.2211 time to fit residues: 9.1073 Evaluate side-chains 20 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain F residue 27 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 53 optimal weight: 0.0070 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.0040 chunk 32 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.3410 ------------------------------------------------------------------------------- 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 = 0.5369 r_free = 0.5369 target = 0.303407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5286 r_free = 0.5286 target = 0.292581 restraints weight = 22869.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5298 r_free = 0.5298 target = 0.293937 restraints weight = 18163.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5306 r_free = 0.5306 target = 0.294938 restraints weight = 15068.867| |-----------------------------------------------------------------------------| r_work (final): 0.5306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0334 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6282 Z= 0.187 Angle : 0.698 8.262 8580 Z= 0.332 Chirality : 0.048 0.115 966 Planarity : 0.006 0.044 1128 Dihedral : 4.051 11.697 894 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 4.81 % Allowed : 14.10 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.27), residues: 792 helix: -0.16 (0.67), residues: 66 sheet: -1.77 (0.42), residues: 144 loop : -2.99 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 76 HIS 0.003 0.001 HIS C 62 PHE 0.015 0.001 PHE F 147 TYR 0.008 0.001 TYR D 132 ARG 0.002 0.000 ARG F 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 22 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 52 average time/residue: 0.1096 time to fit residues: 9.2555 Evaluate side-chains 29 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.0470 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 0.0070 chunk 18 optimal weight: 0.9980 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.5409 r_free = 0.5409 target = 0.299890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5305 r_free = 0.5305 target = 0.290510 restraints weight = 25553.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5323 r_free = 0.5323 target = 0.292256 restraints weight = 19802.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5335 r_free = 0.5335 target = 0.293594 restraints weight = 15685.586| |-----------------------------------------------------------------------------| r_work (final): 0.5334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0509 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6282 Z= 0.188 Angle : 0.703 7.912 8580 Z= 0.337 Chirality : 0.048 0.142 966 Planarity : 0.006 0.040 1128 Dihedral : 4.081 11.358 894 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 2.56 % Allowed : 18.43 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.27), residues: 792 helix: 0.25 (0.72), residues: 66 sheet: -1.82 (0.43), residues: 144 loop : -3.00 (0.22), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 76 HIS 0.003 0.001 HIS E 62 PHE 0.010 0.002 PHE E 147 TYR 0.033 0.003 TYR E 138 ARG 0.003 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 35 average time/residue: 0.1061 time to fit residues: 6.4633 Evaluate side-chains 26 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 16 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 3 optimal weight: 0.0670 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.0050 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.3532 ------------------------------------------------------------------------------- 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 = 0.5418 r_free = 0.5418 target = 0.299730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5323 r_free = 0.5323 target = 0.291115 restraints weight = 25518.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5340 r_free = 0.5340 target = 0.292755 restraints weight = 19984.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5353 r_free = 0.5353 target = 0.294030 restraints weight = 15714.463| |-----------------------------------------------------------------------------| r_work (final): 0.5352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0529 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6282 Z= 0.176 Angle : 0.659 8.154 8580 Z= 0.317 Chirality : 0.047 0.113 966 Planarity : 0.005 0.039 1128 Dihedral : 3.985 10.842 894 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 4.65 % Allowed : 19.39 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.27), residues: 792 helix: 0.49 (0.72), residues: 66 sheet: -1.94 (0.56), residues: 96 loop : -2.91 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 76 HIS 0.002 0.001 HIS E 62 PHE 0.011 0.001 PHE D 147 TYR 0.019 0.002 TYR A 138 ARG 0.004 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 16 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 23 residues processed: 43 average time/residue: 0.1032 time to fit residues: 7.5945 Evaluate side-chains 35 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 12 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 0.1980 chunk 30 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 21 optimal weight: 0.0770 chunk 70 optimal weight: 0.2980 overall best weight: 0.2138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 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 = 0.5416 r_free = 0.5416 target = 0.297551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5325 r_free = 0.5325 target = 0.289253 restraints weight = 25681.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5339 r_free = 0.5339 target = 0.290742 restraints weight = 19868.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5352 r_free = 0.5352 target = 0.292020 restraints weight = 15843.594| |-----------------------------------------------------------------------------| r_work (final): 0.5353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0524 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6282 Z= 0.157 Angle : 0.631 7.931 8580 Z= 0.302 Chirality : 0.046 0.144 966 Planarity : 0.005 0.036 1128 Dihedral : 3.781 11.411 894 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 3.37 % Allowed : 22.12 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.27), residues: 792 helix: 0.35 (0.68), residues: 66 sheet: -1.85 (0.56), residues: 96 loop : -2.91 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 76 HIS 0.001 0.001 HIS E 62 PHE 0.008 0.001 PHE E 147 TYR 0.013 0.001 TYR D 138 ARG 0.001 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 18 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 39 average time/residue: 0.1162 time to fit residues: 7.6839 Evaluate side-chains 26 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 12 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 0.0570 chunk 59 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.0020 chunk 57 optimal weight: 0.0050 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 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 = 0.5417 r_free = 0.5417 target = 0.297891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.289963 restraints weight = 25595.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5345 r_free = 0.5345 target = 0.291382 restraints weight = 19643.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5359 r_free = 0.5359 target = 0.292645 restraints weight = 15207.348| |-----------------------------------------------------------------------------| r_work (final): 0.5360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0553 moved from start: 0.6414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6282 Z= 0.157 Angle : 0.647 9.527 8580 Z= 0.303 Chirality : 0.047 0.195 966 Planarity : 0.005 0.036 1128 Dihedral : 3.736 11.446 894 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 2.40 % Allowed : 24.20 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.26), residues: 792 helix: -0.20 (0.66), residues: 66 sheet: -1.96 (0.54), residues: 96 loop : -2.91 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 76 HIS 0.001 0.001 HIS E 62 PHE 0.007 0.001 PHE A 143 TYR 0.012 0.001 TYR E 138 ARG 0.002 0.000 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 10 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 25 average time/residue: 0.1039 time to fit residues: 4.8929 Evaluate side-chains 24 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 10 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.0470 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 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 = 0.5399 r_free = 0.5399 target = 0.292741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5314 r_free = 0.5314 target = 0.284172 restraints weight = 25558.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.285607 restraints weight = 20170.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5340 r_free = 0.5340 target = 0.286940 restraints weight = 16162.968| |-----------------------------------------------------------------------------| r_work (final): 0.5342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0773 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6282 Z= 0.197 Angle : 0.705 7.930 8580 Z= 0.343 Chirality : 0.049 0.164 966 Planarity : 0.006 0.038 1128 Dihedral : 4.021 13.531 894 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 3.69 % Allowed : 22.92 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.26), residues: 792 helix: -0.16 (0.64), residues: 66 sheet: -1.80 (0.55), residues: 96 loop : -3.00 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 76 HIS 0.006 0.002 HIS E 62 PHE 0.011 0.002 PHE E 147 TYR 0.014 0.002 TYR D 132 ARG 0.007 0.001 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 16 time to evaluate : 0.634 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 21 residues processed: 39 average time/residue: 0.1005 time to fit residues: 6.8852 Evaluate side-chains 30 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 9 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.0470 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 0.0270 chunk 47 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 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 = 0.5404 r_free = 0.5404 target = 0.293023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.5322 r_free = 0.5322 target = 0.284443 restraints weight = 25662.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5333 r_free = 0.5333 target = 0.285731 restraints weight = 20054.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5345 r_free = 0.5345 target = 0.287137 restraints weight = 16265.649| |-----------------------------------------------------------------------------| r_work (final): 0.5347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0807 moved from start: 0.7381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6282 Z= 0.171 Angle : 0.670 7.565 8580 Z= 0.321 Chirality : 0.047 0.156 966 Planarity : 0.005 0.038 1128 Dihedral : 3.898 12.774 894 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.04 % Allowed : 23.08 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.26), residues: 792 helix: -0.37 (0.63), residues: 66 sheet: -1.70 (0.54), residues: 96 loop : -3.01 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 76 HIS 0.003 0.001 HIS B 62 PHE 0.010 0.001 PHE D 147 TYR 0.013 0.002 TYR E 138 ARG 0.002 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 9 time to evaluate : 0.709 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 19 residues processed: 28 average time/residue: 0.1014 time to fit residues: 5.2000 Evaluate side-chains 28 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 9 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 69 optimal weight: 0.0000 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 0.0470 chunk 21 optimal weight: 0.7980 overall best weight: 0.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 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 = 0.5406 r_free = 0.5406 target = 0.293339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5324 r_free = 0.5324 target = 0.284413 restraints weight = 25621.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.5339 r_free = 0.5339 target = 0.286037 restraints weight = 20276.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5352 r_free = 0.5352 target = 0.287546 restraints weight = 16474.701| |-----------------------------------------------------------------------------| r_work (final): 0.5354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0799 moved from start: 0.7786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6282 Z= 0.157 Angle : 0.638 7.691 8580 Z= 0.301 Chirality : 0.047 0.146 966 Planarity : 0.005 0.037 1128 Dihedral : 3.722 13.133 894 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 2.56 % Allowed : 23.56 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.25), residues: 792 helix: -0.53 (0.61), residues: 66 sheet: -1.87 (0.50), residues: 96 loop : -2.99 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 76 HIS 0.002 0.001 HIS C 62 PHE 0.006 0.001 PHE E 147 TYR 0.009 0.002 TYR C 138 ARG 0.003 0.000 ARG D 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 9 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 15 residues processed: 25 average time/residue: 0.1002 time to fit residues: 4.6574 Evaluate side-chains 24 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 9 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 10 optimal weight: 0.3980 chunk 77 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 70 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 = 0.5381 r_free = 0.5381 target = 0.287971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5301 r_free = 0.5301 target = 0.278948 restraints weight = 26314.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5312 r_free = 0.5312 target = 0.280251 restraints weight = 21622.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5323 r_free = 0.5323 target = 0.281342 restraints weight = 18138.239| |-----------------------------------------------------------------------------| r_work (final): 0.5323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1136 moved from start: 0.8931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6282 Z= 0.216 Angle : 0.744 7.577 8580 Z= 0.364 Chirality : 0.049 0.143 966 Planarity : 0.006 0.039 1128 Dihedral : 4.561 15.127 894 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 3.04 % Allowed : 23.08 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.26), residues: 792 helix: -0.97 (0.62), residues: 66 sheet: -0.75 (0.49), residues: 114 loop : -3.12 (0.21), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP F 76 HIS 0.006 0.002 HIS B 62 PHE 0.018 0.003 PHE D 147 TYR 0.020 0.003 TYR B 132 ARG 0.004 0.001 ARG F 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.51 seconds wall clock time: 41 minutes 32.44 seconds (2492.44 seconds total)