Starting phenix.real_space_refine on Sun Mar 10 19:03:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkh_23408/03_2024/7lkh_23408.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkh_23408/03_2024/7lkh_23408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkh_23408/03_2024/7lkh_23408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkh_23408/03_2024/7lkh_23408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkh_23408/03_2024/7lkh_23408.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkh_23408/03_2024/7lkh_23408.pdb" } resolution = 3.5 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 2661 2.51 5 N 717 2.21 5 O 793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 121": "NH1" <-> "NH2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 648": "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 89": "OE1" <-> "OE2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4179 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2338 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 22, 'TRANS': 263} Chain breaks: 2 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: 2.84, per 1000 atoms: 0.68 Number of scatterers: 4179 At special positions: 0 Unit cell: (70.2, 100.44, 88.56, 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 793 8.00 N 717 7.00 C 2661 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=2.04 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: 1.76 Conformation dependent library (CDL) restraints added in 688.8 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 976 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 25.6% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.667A 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: 3.925A 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 Processing helix chain 'A' and resid 688 through 695 Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.745A 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: 3.765A 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: 6.711A pdb=" N VAL A 61 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N HIS A 273 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP A 63 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 8.189A 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: 6.711A pdb=" N VAL A 61 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N HIS A 273 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP A 63 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N HIS A 275 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ILE A 681 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN A 95 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 683 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE A 97 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU A 685 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS A 99 " --> pdb=" O LEU A 685 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU A 687 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 101 " --> pdb=" O LEU A 687 " (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: 6.429A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.802A 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 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.924A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 348 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: 1.90 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: 1038 1.46 - 1.58: 1904 1.58 - 1.71: 0 1.71 - 1.83: 9 Bond restraints: 4284 Sorted by residual: bond pdb=" N VAL A 55 " pdb=" CA VAL A 55 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.19e-02 7.06e+03 1.23e+01 bond pdb=" N THR A 59 " pdb=" CA THR A 59 " ideal model delta sigma weight residual 1.462 1.491 -0.029 8.50e-03 1.38e+04 1.19e+01 bond pdb=" N VAL A 61 " pdb=" CA VAL A 61 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.32e-02 5.74e+03 6.85e+00 bond pdb=" N LYS A 62 " pdb=" CA LYS A 62 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.31e-02 5.83e+03 5.86e+00 bond pdb=" N GLY A 53 " pdb=" CA GLY A 53 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.60e-02 3.91e+03 5.31e+00 ... (remaining 4279 not shown) Histogram of bond angle deviations from ideal: 101.21 - 107.78: 212 107.78 - 114.35: 2382 114.35 - 120.91: 1885 120.91 - 127.48: 1286 127.48 - 134.04: 62 Bond angle restraints: 5827 Sorted by residual: angle pdb=" C LEU L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta sigma weight residual 119.84 113.38 6.46 1.25e+00 6.40e-01 2.67e+01 angle pdb=" C ASP A 83 " pdb=" N TRP A 84 " pdb=" CA TRP A 84 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 angle pdb=" CA VAL A 61 " pdb=" C VAL A 61 " pdb=" O VAL A 61 " ideal model delta sigma weight residual 121.59 117.51 4.08 1.03e+00 9.43e-01 1.57e+01 angle pdb=" CA LYS A 62 " pdb=" C LYS A 62 " pdb=" O LYS A 62 " ideal model delta sigma weight residual 121.81 117.32 4.49 1.18e+00 7.18e-01 1.45e+01 angle pdb=" CA ARG A 673 " pdb=" C ARG A 673 " pdb=" O ARG A 673 " ideal model delta sigma weight residual 121.60 117.02 4.58 1.21e+00 6.83e-01 1.43e+01 ... (remaining 5822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 2350 16.91 - 33.81: 185 33.81 - 50.71: 35 50.71 - 67.62: 6 67.62 - 84.52: 8 Dihedral angle restraints: 2584 sinusoidal: 1070 harmonic: 1514 Sorted by residual: 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 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+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 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ARG H 98 " pdb=" C ARG H 98 " pdb=" N TYR H 99 " pdb=" CA TYR H 99 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 2581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 421 0.042 - 0.084: 140 0.084 - 0.126: 65 0.126 - 0.169: 19 0.169 - 0.211: 3 Chirality restraints: 648 Sorted by residual: chirality pdb=" CA LYS A 256 " pdb=" N LYS A 256 " pdb=" C LYS A 256 " pdb=" CB LYS A 256 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA PHE A 65 " pdb=" N PHE A 65 " pdb=" C PHE A 65 " pdb=" CB PHE A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ARG L 53 " pdb=" N ARG L 53 " pdb=" C ARG L 53 " pdb=" CB ARG L 53 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 645 not shown) Planarity restraints: 744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG H 40 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO H 41 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 154 " -0.065 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO A 155 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 155 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 155 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 65 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO A 66 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.032 5.00e-02 4.00e+02 ... (remaining 741 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 26 2.50 - 3.10: 3058 3.10 - 3.70: 5794 3.70 - 4.30: 8688 4.30 - 4.90: 14923 Nonbonded interactions: 32489 Sorted by model distance: nonbonded pdb=" O4 NAG B 1 " pdb=" O7 NAG B 2 " model vdw 1.903 2.440 nonbonded pdb=" OD2 ASP H 73 " pdb=" OG SER H 76 " model vdw 2.057 2.440 nonbonded pdb=" O GLY A 87 " pdb=" OH TYR A 674 " model vdw 2.096 2.440 nonbonded pdb=" O ASN L 77 " pdb=" OD1 ASN L 77 " model vdw 2.245 3.040 nonbonded pdb=" O PHE A 276 " pdb=" O ALA A 671 " model vdw 2.276 3.040 ... (remaining 32484 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 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.420 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.670 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 4284 Z= 0.388 Angle : 0.938 9.116 5827 Z= 0.565 Chirality : 0.054 0.211 648 Planarity : 0.007 0.112 743 Dihedral : 13.326 84.519 1599 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.22 % Allowed : 0.43 % Favored : 99.35 % 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: -0.99 (0.37), residues: 506 helix: -0.11 (0.59), residues: 80 sheet: -0.14 (0.39), residues: 171 loop : -1.16 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.004 0.001 HIS A 273 PHE 0.037 0.003 PHE A 65 TYR 0.031 0.003 TYR A 64 ARG 0.013 0.001 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.483 Fit side-chains REVERT: A 138 SER cc_start: 0.8344 (t) cc_final: 0.8138 (t) REVERT: L 108 ARG cc_start: 0.4258 (ppt170) cc_final: 0.4046 (ppt170) outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.1920 time to fit residues: 18.8332 Evaluate side-chains 52 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 25 optimal weight: 0.0170 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 167 HIS ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 37 GLN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4284 Z= 0.189 Angle : 0.668 14.354 5827 Z= 0.328 Chirality : 0.046 0.157 648 Planarity : 0.005 0.068 743 Dihedral : 6.173 58.709 613 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.74 % Allowed : 6.09 % Favored : 92.17 % 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: -0.45 (0.37), residues: 506 helix: 0.33 (0.62), residues: 72 sheet: 0.03 (0.38), residues: 165 loop : -0.61 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 84 HIS 0.004 0.001 HIS A 167 PHE 0.010 0.001 PHE L 98 TYR 0.035 0.002 TYR H 99 ARG 0.006 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.517 Fit side-chains REVERT: A 62 LYS cc_start: 0.7280 (mttt) cc_final: 0.6671 (mppt) REVERT: A 272 VAL cc_start: 0.8721 (t) cc_final: 0.8470 (t) REVERT: H 87 THR cc_start: 0.7649 (t) cc_final: 0.7421 (p) outliers start: 8 outliers final: 4 residues processed: 73 average time/residue: 0.1414 time to fit residues: 13.5949 Evaluate side-chains 56 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 149 GLN A 176 ASN ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4284 Z= 0.208 Angle : 0.637 12.545 5827 Z= 0.316 Chirality : 0.045 0.159 648 Planarity : 0.005 0.053 743 Dihedral : 5.889 59.019 611 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.39 % Allowed : 8.91 % Favored : 88.70 % 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 (0.38), residues: 506 helix: 0.59 (0.62), residues: 72 sheet: 0.13 (0.39), residues: 167 loop : -0.41 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 84 HIS 0.002 0.001 HIS A 198 PHE 0.008 0.001 PHE A 663 TYR 0.032 0.002 TYR H 99 ARG 0.003 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.508 Fit side-chains REVERT: A 62 LYS cc_start: 0.7443 (mttt) cc_final: 0.6271 (mttt) outliers start: 11 outliers final: 7 residues processed: 77 average time/residue: 0.1614 time to fit residues: 15.8825 Evaluate side-chains 61 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4284 Z= 0.195 Angle : 0.628 12.841 5827 Z= 0.306 Chirality : 0.044 0.154 648 Planarity : 0.005 0.044 743 Dihedral : 5.807 57.644 611 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.61 % Allowed : 11.30 % Favored : 86.09 % 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: -0.03 (0.39), residues: 506 helix: 0.61 (0.60), residues: 74 sheet: 0.10 (0.39), residues: 167 loop : -0.17 (0.42), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 84 HIS 0.003 0.001 HIS A 198 PHE 0.008 0.001 PHE L 98 TYR 0.027 0.002 TYR H 99 ARG 0.003 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.511 Fit side-chains REVERT: A 62 LYS cc_start: 0.7380 (mttt) cc_final: 0.6413 (mppt) REVERT: H 91 THR cc_start: 0.8722 (p) cc_final: 0.8499 (p) REVERT: L 28 ASP cc_start: 0.7864 (p0) cc_final: 0.7548 (p0) outliers start: 12 outliers final: 9 residues processed: 69 average time/residue: 0.1434 time to fit residues: 13.1348 Evaluate side-chains 66 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 44 VAL 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: 0.1980 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4284 Z= 0.183 Angle : 0.607 12.055 5827 Z= 0.295 Chirality : 0.043 0.150 648 Planarity : 0.004 0.040 743 Dihedral : 5.699 54.787 611 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.26 % Allowed : 11.74 % Favored : 85.00 % 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: 0.01 (0.39), residues: 506 helix: 0.54 (0.60), residues: 75 sheet: 0.12 (0.39), residues: 170 loop : -0.11 (0.43), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 84 HIS 0.008 0.001 HIS A 198 PHE 0.008 0.001 PHE A 663 TYR 0.026 0.002 TYR H 99 ARG 0.003 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.458 Fit side-chains REVERT: A 62 LYS cc_start: 0.7305 (mttt) cc_final: 0.6000 (mptt) REVERT: H 91 THR cc_start: 0.8709 (p) cc_final: 0.8501 (p) REVERT: L 28 ASP cc_start: 0.7876 (p0) cc_final: 0.7585 (p0) outliers start: 15 outliers final: 13 residues processed: 74 average time/residue: 0.1318 time to fit residues: 12.9948 Evaluate side-chains 77 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 4 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4284 Z= 0.173 Angle : 0.589 11.784 5827 Z= 0.288 Chirality : 0.043 0.146 648 Planarity : 0.004 0.040 743 Dihedral : 5.593 49.955 611 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.13 % Allowed : 11.52 % Favored : 84.35 % 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: 0.04 (0.39), residues: 506 helix: 0.57 (0.59), residues: 75 sheet: 0.21 (0.40), residues: 169 loop : -0.14 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 84 HIS 0.008 0.001 HIS A 198 PHE 0.007 0.001 PHE A 663 TYR 0.025 0.002 TYR H 99 ARG 0.003 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.438 Fit side-chains REVERT: H 91 THR cc_start: 0.8722 (p) cc_final: 0.8516 (p) REVERT: L 28 ASP cc_start: 0.7935 (p0) cc_final: 0.7677 (p0) outliers start: 19 outliers final: 17 residues processed: 76 average time/residue: 0.1404 time to fit residues: 14.2624 Evaluate side-chains 74 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 57 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN A 180 ASN H 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4284 Z= 0.243 Angle : 0.639 11.072 5827 Z= 0.313 Chirality : 0.044 0.144 648 Planarity : 0.004 0.044 743 Dihedral : 5.707 48.588 611 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.91 % Allowed : 13.26 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.39), residues: 506 helix: 0.32 (0.58), residues: 75 sheet: 0.19 (0.39), residues: 168 loop : -0.16 (0.43), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 84 HIS 0.008 0.001 HIS A 198 PHE 0.013 0.001 PHE L 87 TYR 0.026 0.002 TYR H 99 ARG 0.002 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.497 Fit side-chains REVERT: H 91 THR cc_start: 0.8745 (p) cc_final: 0.8534 (p) REVERT: L 28 ASP cc_start: 0.8012 (p0) cc_final: 0.7782 (p0) outliers start: 18 outliers final: 15 residues processed: 72 average time/residue: 0.1476 time to fit residues: 13.8548 Evaluate side-chains 73 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4284 Z= 0.224 Angle : 0.629 11.035 5827 Z= 0.309 Chirality : 0.044 0.148 648 Planarity : 0.004 0.044 743 Dihedral : 5.647 49.178 611 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.26 % Allowed : 14.13 % Favored : 82.61 % 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: -0.17 (0.39), residues: 506 helix: 0.04 (0.55), residues: 81 sheet: 0.15 (0.39), residues: 168 loop : -0.23 (0.43), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 84 HIS 0.011 0.001 HIS A 198 PHE 0.015 0.001 PHE A 65 TYR 0.026 0.002 TYR H 99 ARG 0.007 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.484 Fit side-chains REVERT: H 91 THR cc_start: 0.8751 (p) cc_final: 0.8542 (p) REVERT: L 28 ASP cc_start: 0.8027 (p0) cc_final: 0.7809 (p0) outliers start: 15 outliers final: 15 residues processed: 68 average time/residue: 0.1402 time to fit residues: 12.6525 Evaluate side-chains 72 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4284 Z= 0.196 Angle : 0.600 10.967 5827 Z= 0.297 Chirality : 0.043 0.150 648 Planarity : 0.004 0.043 743 Dihedral : 5.531 52.546 611 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.04 % Allowed : 14.13 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.39), residues: 506 helix: 0.34 (0.58), residues: 75 sheet: 0.17 (0.40), residues: 168 loop : -0.21 (0.42), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 84 HIS 0.010 0.001 HIS A 198 PHE 0.014 0.001 PHE L 87 TYR 0.024 0.002 TYR H 99 ARG 0.007 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.465 Fit side-chains REVERT: H 91 THR cc_start: 0.8732 (p) cc_final: 0.8520 (p) outliers start: 14 outliers final: 14 residues processed: 73 average time/residue: 0.1377 time to fit residues: 13.4028 Evaluate side-chains 78 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.0370 chunk 39 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN H 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4284 Z= 0.169 Angle : 0.603 11.028 5827 Z= 0.295 Chirality : 0.043 0.143 648 Planarity : 0.004 0.043 743 Dihedral : 5.469 57.505 611 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.83 % Allowed : 14.78 % Favored : 82.39 % 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: 0.01 (0.39), residues: 506 helix: 0.37 (0.59), residues: 75 sheet: 0.40 (0.41), residues: 161 loop : -0.26 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 84 HIS 0.007 0.001 HIS A 198 PHE 0.008 0.001 PHE A 65 TYR 0.023 0.001 TYR H 99 ARG 0.006 0.000 ARG A 267 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.528 Fit side-chains REVERT: H 91 THR cc_start: 0.8726 (p) cc_final: 0.8516 (p) outliers start: 13 outliers final: 13 residues processed: 71 average time/residue: 0.1303 time to fit residues: 12.4569 Evaluate side-chains 73 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.0670 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN H 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.145022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117876 restraints weight = 5696.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120972 restraints weight = 3637.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123152 restraints weight = 2717.353| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4284 Z= 0.164 Angle : 0.589 10.975 5827 Z= 0.291 Chirality : 0.042 0.147 648 Planarity : 0.004 0.043 743 Dihedral : 5.481 59.792 611 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.70 % Allowed : 13.91 % Favored : 82.39 % 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: 0.04 (0.39), residues: 506 helix: 0.39 (0.59), residues: 75 sheet: 0.42 (0.41), residues: 161 loop : -0.24 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 84 HIS 0.009 0.001 HIS A 198 PHE 0.015 0.001 PHE L 87 TYR 0.023 0.001 TYR H 99 ARG 0.006 0.000 ARG A 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1229.73 seconds wall clock time: 25 minutes 19.64 seconds (1519.64 seconds total)