Starting phenix.real_space_refine on Wed Jan 17 15:22:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkf_23405/01_2024/7lkf_23405.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkf_23405/01_2024/7lkf_23405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkf_23405/01_2024/7lkf_23405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkf_23405/01_2024/7lkf_23405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkf_23405/01_2024/7lkf_23405.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkf_23405/01_2024/7lkf_23405.pdb" } resolution = 2.9 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= 0.005 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 8 5.16 5 C 2634 2.51 5 N 710 2.21 5 O 787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 56": "OE1" <-> "OE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 638": "OE1" <-> "OE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A ARG 657": "NH1" <-> "NH2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 4139 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2298 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 22, 'TRANS': 258} Chain breaks: 3 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 854 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.81, per 1000 atoms: 0.68 Number of scatterers: 4139 At special positions: 0 Unit cell: (74.52, 91.8, 95.04, 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 8 16.00 O 787 8.00 N 710 7.00 C 2634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 667 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 790.3 milliseconds 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 964 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 25.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.716A pdb=" N ARG A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.899A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 657 through 665 removed outlier: 3.601A pdb=" N TYR A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 695 Processing helix chain 'A' and resid 697 through 701 removed outlier: 3.513A pdb=" N ALA A 701 " --> pdb=" O PRO A 698 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.777A pdb=" N GLN H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.831A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 64 removed outlier: 6.301A pdb=" N VAL A 61 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N HIS A 273 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP A 63 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N HIS A 275 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 64 removed outlier: 6.301A pdb=" N VAL A 61 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N HIS A 273 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP A 63 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N HIS A 275 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.473A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.562A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.748A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 384 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: 1.17 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1333 1.34 - 1.46: 774 1.46 - 1.57: 2127 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 4243 Sorted by residual: bond pdb=" N GLY A 636 " pdb=" CA GLY A 636 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.49e+00 bond pdb=" N GLY A 53 " pdb=" CA GLY A 53 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.13e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.70e+00 ... (remaining 4238 not shown) Histogram of bond angle deviations from ideal: 101.27 - 107.83: 203 107.83 - 114.39: 2390 114.39 - 120.96: 1859 120.96 - 127.52: 1256 127.52 - 134.08: 61 Bond angle restraints: 5769 Sorted by residual: angle pdb=" CA PRO A 155 " pdb=" N PRO A 155 " pdb=" CD PRO A 155 " ideal model delta sigma weight residual 112.00 107.82 4.18 1.40e+00 5.10e-01 8.91e+00 angle pdb=" CA TYR H 99 " pdb=" CB TYR H 99 " pdb=" CG TYR H 99 " ideal model delta sigma weight residual 113.90 118.96 -5.06 1.80e+00 3.09e-01 7.91e+00 angle pdb=" N ASP H 103 " pdb=" CA ASP H 103 " pdb=" C ASP H 103 " ideal model delta sigma weight residual 113.18 109.67 3.51 1.33e+00 5.65e-01 6.95e+00 angle pdb=" N ASP A 190 " pdb=" CA ASP A 190 " pdb=" C ASP A 190 " ideal model delta sigma weight residual 107.37 112.16 -4.79 2.07e+00 2.33e-01 5.35e+00 angle pdb=" N THR L 51 " pdb=" CA THR L 51 " pdb=" C THR L 51 " ideal model delta sigma weight residual 110.80 115.21 -4.41 2.13e+00 2.20e-01 4.30e+00 ... (remaining 5764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 2362 17.68 - 35.36: 158 35.36 - 53.04: 20 53.04 - 70.72: 9 70.72 - 88.40: 7 Dihedral angle restraints: 2556 sinusoidal: 1060 harmonic: 1496 Sorted by residual: dihedral pdb=" CB CYS A 147 " pdb=" SG CYS A 147 " pdb=" SG CYS A 169 " pdb=" CB CYS A 169 " ideal model delta sinusoidal sigma weight residual -86.00 -162.43 76.43 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CA THR L 93 " pdb=" C THR L 93 " pdb=" N LEU L 94 " pdb=" CA LEU L 94 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA PRO A 155 " pdb=" C PRO A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 2553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 550 0.062 - 0.124: 80 0.124 - 0.186: 8 0.186 - 0.248: 0 0.248 - 0.310: 1 Chirality restraints: 639 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 667 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA LEU L 94 " pdb=" N LEU L 94 " pdb=" C LEU L 94 " pdb=" CB LEU L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 636 not shown) Planarity restraints: 737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 154 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO A 155 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 155 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 155 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 117 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 118 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 99 " -0.002 2.00e-02 2.50e+03 1.08e-02 2.33e+00 pdb=" CG TYR H 99 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR H 99 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR H 99 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR H 99 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 99 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR H 99 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 99 " -0.001 2.00e-02 2.50e+03 ... (remaining 734 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 56 2.66 - 3.22: 3758 3.22 - 3.78: 5969 3.78 - 4.34: 8951 4.34 - 4.90: 14737 Nonbonded interactions: 33471 Sorted by model distance: nonbonded pdb=" O3 NAG B 1 " pdb=" O7 NAG B 2 " model vdw 2.101 2.440 nonbonded pdb=" O GLY A 87 " pdb=" OH TYR A 674 " model vdw 2.199 2.440 nonbonded pdb=" O ARG A 161 " pdb=" OD1 ASN A 162 " model vdw 2.350 3.040 nonbonded pdb=" OD1 ASP L 17 " pdb=" N ARG L 18 " model vdw 2.358 2.520 nonbonded pdb=" O ASN L 31 " pdb=" OG1 THR L 51 " model vdw 2.393 2.440 ... (remaining 33466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 4.440 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.520 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.005 0.062 4243 Z= 0.299 Angle : 0.666 6.936 5769 Z= 0.374 Chirality : 0.047 0.310 639 Planarity : 0.005 0.105 736 Dihedral : 12.764 88.404 1583 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: -0.59 (0.37), residues: 499 helix: 0.37 (0.64), residues: 73 sheet: -0.29 (0.39), residues: 173 loop : -0.59 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 110 HIS 0.004 0.001 HIS A 273 PHE 0.021 0.002 PHE A 97 TYR 0.022 0.002 TYR H 99 ARG 0.012 0.001 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.476 Fit side-chains REVERT: A 128 GLU cc_start: 0.7583 (tp30) cc_final: 0.7380 (tp30) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 1.6089 time to fit residues: 137.2326 Evaluate side-chains 56 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 697 HIS H 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4243 Z= 0.230 Angle : 0.604 6.778 5769 Z= 0.305 Chirality : 0.046 0.176 639 Planarity : 0.004 0.052 736 Dihedral : 5.118 25.581 605 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.32 % Allowed : 11.21 % Favored : 87.47 % 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: -0.32 (0.38), residues: 499 helix: 0.46 (0.65), residues: 73 sheet: -0.21 (0.39), residues: 172 loop : -0.28 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 96 HIS 0.004 0.001 HIS A 273 PHE 0.021 0.001 PHE A 97 TYR 0.036 0.002 TYR H 99 ARG 0.003 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.392 Fit side-chains REVERT: A 128 GLU cc_start: 0.7447 (tp30) cc_final: 0.7176 (tp30) outliers start: 6 outliers final: 2 residues processed: 62 average time/residue: 1.1078 time to fit residues: 70.7170 Evaluate side-chains 55 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 GLN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4243 Z= 0.212 Angle : 0.578 7.321 5769 Z= 0.290 Chirality : 0.045 0.173 639 Planarity : 0.004 0.038 736 Dihedral : 4.867 23.651 605 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.76 % Allowed : 13.41 % Favored : 84.84 % 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: -0.23 (0.38), residues: 499 helix: 0.51 (0.65), residues: 73 sheet: -0.25 (0.38), residues: 172 loop : -0.14 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS A 273 PHE 0.019 0.001 PHE A 97 TYR 0.027 0.002 TYR H 99 ARG 0.004 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.469 Fit side-chains REVERT: A 277 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7739 (mtpp) REVERT: L 45 LYS cc_start: 0.8689 (tttt) cc_final: 0.8330 (tttp) outliers start: 8 outliers final: 4 residues processed: 63 average time/residue: 1.4384 time to fit residues: 93.5560 Evaluate side-chains 55 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4243 Z= 0.345 Angle : 0.650 9.176 5769 Z= 0.324 Chirality : 0.048 0.174 639 Planarity : 0.005 0.036 736 Dihedral : 5.142 25.574 605 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.30 % Allowed : 13.63 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.38), residues: 499 helix: 0.36 (0.64), residues: 73 sheet: -0.30 (0.39), residues: 172 loop : -0.19 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.003 0.001 HIS A 273 PHE 0.026 0.002 PHE A 97 TYR 0.028 0.002 TYR H 99 ARG 0.004 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.492 Fit side-chains REVERT: L 45 LYS cc_start: 0.8708 (tttt) cc_final: 0.8410 (tttp) outliers start: 15 outliers final: 7 residues processed: 66 average time/residue: 1.4620 time to fit residues: 99.5093 Evaluate side-chains 56 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4243 Z= 0.297 Angle : 0.618 7.857 5769 Z= 0.310 Chirality : 0.046 0.174 639 Planarity : 0.004 0.034 736 Dihedral : 5.065 25.162 605 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.08 % Allowed : 14.73 % Favored : 82.20 % 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: -0.29 (0.39), residues: 499 helix: 0.37 (0.64), residues: 73 sheet: -0.19 (0.40), residues: 166 loop : -0.23 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.003 0.001 HIS A 273 PHE 0.020 0.002 PHE A 97 TYR 0.031 0.002 TYR H 99 ARG 0.004 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.501 Fit side-chains REVERT: L 45 LYS cc_start: 0.8708 (tttt) cc_final: 0.8417 (tttp) outliers start: 14 outliers final: 9 residues processed: 60 average time/residue: 1.4248 time to fit residues: 88.3328 Evaluate side-chains 56 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.0060 chunk 35 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 65 GLN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4243 Z= 0.177 Angle : 0.552 7.000 5769 Z= 0.277 Chirality : 0.043 0.179 639 Planarity : 0.004 0.040 736 Dihedral : 4.718 22.572 605 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.64 % Allowed : 16.26 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.39), residues: 499 helix: 0.59 (0.66), residues: 73 sheet: -0.15 (0.39), residues: 166 loop : -0.11 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS A 273 PHE 0.010 0.001 PHE A 97 TYR 0.032 0.001 TYR H 99 ARG 0.006 0.000 ARG H 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.511 Fit side-chains REVERT: L 45 LYS cc_start: 0.8690 (tttt) cc_final: 0.8411 (tttp) outliers start: 12 outliers final: 7 residues processed: 61 average time/residue: 1.4815 time to fit residues: 93.2841 Evaluate side-chains 55 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.0170 chunk 32 optimal weight: 1.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN H 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4243 Z= 0.277 Angle : 0.637 15.511 5769 Z= 0.313 Chirality : 0.046 0.173 639 Planarity : 0.005 0.040 736 Dihedral : 4.892 24.289 605 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.74 % Allowed : 16.26 % Favored : 80.00 % 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: -0.19 (0.39), residues: 499 helix: 0.53 (0.65), residues: 73 sheet: -0.15 (0.40), residues: 166 loop : -0.17 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS A 658 PHE 0.017 0.002 PHE A 97 TYR 0.036 0.002 TYR H 99 ARG 0.007 0.000 ARG H 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 50 time to evaluate : 0.485 Fit side-chains REVERT: A 64 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: A 109 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8826 (m-10) REVERT: H 89 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: L 45 LYS cc_start: 0.8700 (tttt) cc_final: 0.8420 (tttp) outliers start: 17 outliers final: 8 residues processed: 64 average time/residue: 1.3251 time to fit residues: 87.6348 Evaluate side-chains 59 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4243 Z= 0.157 Angle : 0.589 16.968 5769 Z= 0.283 Chirality : 0.043 0.181 639 Planarity : 0.004 0.038 736 Dihedral : 4.546 22.030 605 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.42 % Allowed : 17.58 % Favored : 80.00 % 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: -0.05 (0.39), residues: 499 helix: 0.71 (0.66), residues: 73 sheet: -0.11 (0.39), residues: 166 loop : -0.07 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS A 275 PHE 0.008 0.001 PHE A 97 TYR 0.033 0.001 TYR H 99 ARG 0.007 0.000 ARG H 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.551 Fit side-chains REVERT: H 65 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8113 (mm-40) REVERT: L 45 LYS cc_start: 0.8649 (tttt) cc_final: 0.8363 (tttp) outliers start: 11 outliers final: 4 residues processed: 59 average time/residue: 1.6316 time to fit residues: 99.2171 Evaluate side-chains 50 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 673 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.0070 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4243 Z= 0.146 Angle : 0.566 14.057 5769 Z= 0.274 Chirality : 0.043 0.182 639 Planarity : 0.004 0.032 736 Dihedral : 4.318 21.432 605 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.32 % Allowed : 18.68 % Favored : 80.00 % 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: -0.06 (0.39), residues: 499 helix: 0.75 (0.66), residues: 74 sheet: -0.03 (0.39), residues: 167 loop : -0.16 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 96 HIS 0.002 0.001 HIS A 275 PHE 0.007 0.001 PHE L 98 TYR 0.031 0.001 TYR H 99 ARG 0.004 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.510 Fit side-chains REVERT: L 45 LYS cc_start: 0.8560 (tttt) cc_final: 0.8295 (tttt) outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 1.3458 time to fit residues: 79.3899 Evaluate side-chains 52 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 673 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4243 Z= 0.219 Angle : 0.603 14.016 5769 Z= 0.294 Chirality : 0.045 0.189 639 Planarity : 0.004 0.031 736 Dihedral : 4.547 23.169 605 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.76 % Allowed : 18.46 % Favored : 79.78 % 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: -0.09 (0.39), residues: 499 helix: 0.66 (0.65), residues: 74 sheet: -0.09 (0.40), residues: 166 loop : -0.13 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 96 HIS 0.002 0.001 HIS A 273 PHE 0.012 0.001 PHE A 97 TYR 0.035 0.002 TYR H 99 ARG 0.005 0.000 ARG A 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.501 Fit side-chains REVERT: L 45 LYS cc_start: 0.8624 (tttt) cc_final: 0.8337 (tttt) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 1.4000 time to fit residues: 78.2281 Evaluate side-chains 52 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.122595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.094465 restraints weight = 5203.565| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.39 r_work: 0.2919 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4243 Z= 0.215 Angle : 0.595 13.577 5769 Z= 0.291 Chirality : 0.045 0.178 639 Planarity : 0.004 0.031 736 Dihedral : 4.583 22.651 605 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.32 % Allowed : 19.34 % Favored : 79.34 % 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: -0.12 (0.39), residues: 499 helix: 0.64 (0.65), residues: 74 sheet: -0.13 (0.39), residues: 166 loop : -0.13 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 96 HIS 0.002 0.001 HIS A 275 PHE 0.012 0.001 PHE A 97 TYR 0.038 0.002 TYR H 99 ARG 0.004 0.000 ARG A 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2166.63 seconds wall clock time: 41 minutes 19.01 seconds (2479.01 seconds total)