Starting phenix.real_space_refine on Wed Oct 9 19:00:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs3_38613/10_2024/8xs3_38613.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs3_38613/10_2024/8xs3_38613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs3_38613/10_2024/8xs3_38613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs3_38613/10_2024/8xs3_38613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs3_38613/10_2024/8xs3_38613.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs3_38613/10_2024/8xs3_38613.cif" } resolution = 3.46 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= -0.001 sd= 0.016 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 22 5.16 5 C 2572 2.51 5 N 691 2.21 5 O 833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 4118 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Chain: "B" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1680 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain: "C" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 809 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain breaks: 2 Chain: "D" 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 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.08, per 1000 atoms: 0.99 Number of scatterers: 4118 At special positions: 0 Unit cell: (55.89, 79.35, 109.71, 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 22 16.00 O 833 8.00 N 691 7.00 C 2572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 110 " distance=2.03 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 125 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 301 " - " ASN C 94 " " NAG D 1 " - " ASN C 120 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 556.5 milliseconds 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 990 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 14 sheets defined 7.9% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.857A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 208 through 211 Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.573A pdb=" N GLY C 103 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.504A pdb=" N ILE A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.913A pdb=" N GLY A 146 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR A 183 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.913A pdb=" N GLY A 146 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR A 183 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 158 through 161 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.576A pdb=" N ASP B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.087A pdb=" N LEU B 11 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 120 through 124 removed outlier: 6.054A pdb=" N TYR B 179 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 156 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AB3, first strand: chain 'C' and resid 43 through 45 Processing sheet with id=AB4, first strand: chain 'C' and resid 76 through 77 removed outlier: 3.767A pdb=" N TYR C 91 " --> pdb=" O CYS C 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 99 167 hydrogen bonds defined for protein. 417 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: 1.14 Time building geometry restraints manager: 1.20 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: 1317 1.34 - 1.46: 1004 1.46 - 1.58: 1856 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 4205 Sorted by residual: bond pdb=" C PHE A 129 " pdb=" N PRO A 130 " ideal model delta sigma weight residual 1.335 1.319 0.016 8.70e-03 1.32e+04 3.53e+00 bond pdb=" C LYS A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.336 1.355 -0.020 1.08e-02 8.57e+03 3.27e+00 bond pdb=" C LEU A 131 " pdb=" N ALA A 132 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.47e-02 4.63e+03 2.45e+00 bond pdb=" C3 NAG D 1 " pdb=" O3 NAG D 1 " ideal model delta sigma weight residual 1.403 1.433 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sigma weight residual 1.403 1.431 -0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 4200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 5463 1.67 - 3.34: 219 3.34 - 5.01: 27 5.01 - 6.68: 3 6.68 - 8.35: 2 Bond angle restraints: 5714 Sorted by residual: angle pdb=" N ILE A 102 " pdb=" CA ILE A 102 " pdb=" C ILE A 102 " ideal model delta sigma weight residual 113.71 109.19 4.52 9.50e-01 1.11e+00 2.26e+01 angle pdb=" N LEU B 97 " pdb=" CA LEU B 97 " pdb=" C LEU B 97 " ideal model delta sigma weight residual 113.88 109.74 4.14 1.23e+00 6.61e-01 1.13e+01 angle pdb=" CA VAL C 93 " pdb=" C VAL C 93 " pdb=" N ASN C 94 " ideal model delta sigma weight residual 115.45 118.84 -3.39 1.18e+00 7.18e-01 8.27e+00 angle pdb=" C5 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 111.70 103.35 8.35 3.00e+00 1.11e-01 7.74e+00 angle pdb=" N ARG A 67 " pdb=" CA ARG A 67 " pdb=" C ARG A 67 " ideal model delta sigma weight residual 114.39 110.50 3.89 1.45e+00 4.76e-01 7.19e+00 ... (remaining 5709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2372 17.99 - 35.99: 165 35.99 - 53.98: 28 53.98 - 71.97: 9 71.97 - 89.96: 4 Dihedral angle restraints: 2578 sinusoidal: 1035 harmonic: 1543 Sorted by residual: dihedral pdb=" CA ASN B 143 " pdb=" C ASN B 143 " pdb=" N ASN B 144 " pdb=" CA ASN B 144 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA TRP A 161 " pdb=" C TRP A 161 " pdb=" N ASN A 162 " pdb=" CA ASN A 162 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASN A 162 " pdb=" C ASN A 162 " pdb=" N SER A 163 " pdb=" CA SER A 163 " ideal model delta harmonic sigma weight residual 180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 2575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 462 0.040 - 0.079: 129 0.079 - 0.119: 50 0.119 - 0.158: 15 0.158 - 0.198: 1 Chirality restraints: 657 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.57e+01 chirality pdb=" CA ASN C 120 " pdb=" N ASN C 120 " pdb=" C ASN C 120 " pdb=" CB ASN C 120 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" C1 NAG C 301 " pdb=" ND2 ASN C 94 " pdb=" C2 NAG C 301 " pdb=" O5 NAG C 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 654 not shown) Planarity restraints: 729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 301 " 0.322 2.00e-02 2.50e+03 2.73e-01 9.34e+02 pdb=" C7 NAG C 301 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG C 301 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG C 301 " -0.475 2.00e-02 2.50e+03 pdb=" O7 NAG C 301 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.295 2.00e-02 2.50e+03 2.55e-01 8.13e+02 pdb=" C7 NAG D 2 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.005 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.438 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.260 2.00e-02 2.50e+03 2.20e-01 6.07e+02 pdb=" C7 NAG D 1 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.376 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.012 2.00e-02 2.50e+03 ... (remaining 726 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 85 2.65 - 3.21: 4023 3.21 - 3.78: 6293 3.78 - 4.34: 8188 4.34 - 4.90: 13446 Nonbonded interactions: 32035 Sorted by model distance: nonbonded pdb=" NE2 GLN A 6 " pdb=" O GLN A 112 " model vdw 2.090 3.120 nonbonded pdb=" OE1 GLU B 39 " pdb=" OH TYR B 41 " model vdw 2.178 3.040 nonbonded pdb=" O HIS A 171 " pdb=" OG SER A 187 " model vdw 2.201 3.040 nonbonded pdb=" NZ LYS A 216 " pdb=" O ARG A 217 " model vdw 2.203 3.120 nonbonded pdb=" NH1 ARG A 98 " pdb=" O ARG A 99 " model vdw 2.213 3.120 ... (remaining 32030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.220 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 0.044 4205 Z= 0.314 Angle : 0.765 8.346 5714 Z= 0.442 Chirality : 0.045 0.198 657 Planarity : 0.017 0.273 727 Dihedral : 13.189 89.965 1570 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.31), residues: 521 helix: -3.54 (0.53), residues: 29 sheet: -0.81 (0.33), residues: 204 loop : -2.83 (0.29), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 40 HIS 0.002 0.001 HIS B 195 PHE 0.013 0.001 PHE C 108 TYR 0.015 0.002 TYR B 146 ARG 0.005 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8516 (mt-10) REVERT: B 173 ASP cc_start: 0.8339 (t0) cc_final: 0.8124 (t70) REVERT: B 191 ASP cc_start: 0.9434 (t70) cc_final: 0.9158 (t0) REVERT: B 217 ARG cc_start: 0.8380 (mtm180) cc_final: 0.8171 (mtm180) REVERT: C 75 MET cc_start: 0.7929 (mmt) cc_final: 0.6714 (mmm) REVERT: C 91 TYR cc_start: 0.8305 (m-80) cc_final: 0.7863 (m-10) REVERT: C 97 MET cc_start: 0.9148 (tmm) cc_final: 0.8743 (tmm) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.2351 time to fit residues: 12.3506 Evaluate side-chains 30 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 178 GLN A 204 ASN B 95 GLN C 58 ASN C 70 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4205 Z= 0.230 Angle : 0.645 6.537 5714 Z= 0.329 Chirality : 0.044 0.139 657 Planarity : 0.004 0.051 727 Dihedral : 5.590 34.869 631 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.64 % Allowed : 10.87 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.33), residues: 521 helix: -1.99 (0.66), residues: 30 sheet: -0.39 (0.33), residues: 210 loop : -2.32 (0.32), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 40 HIS 0.001 0.000 HIS B 195 PHE 0.009 0.001 PHE A 153 TYR 0.013 0.002 TYR C 107 ARG 0.003 0.001 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 ASP cc_start: 0.8259 (t0) cc_final: 0.7956 (t0) REVERT: B 217 ARG cc_start: 0.8485 (mtm180) cc_final: 0.8093 (mtm180) REVERT: C 26 MET cc_start: 0.8652 (tpp) cc_final: 0.7844 (pmm) REVERT: C 75 MET cc_start: 0.7726 (mmt) cc_final: 0.6644 (mmm) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.2175 time to fit residues: 9.9619 Evaluate side-chains 28 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain C residue 64 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 47 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4205 Z= 0.142 Angle : 0.583 6.268 5714 Z= 0.296 Chirality : 0.043 0.131 657 Planarity : 0.004 0.051 727 Dihedral : 4.737 22.953 631 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.28 % Allowed : 12.37 % Favored : 86.35 % 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: -1.62 (0.34), residues: 521 helix: -1.45 (0.73), residues: 36 sheet: 0.03 (0.33), residues: 214 loop : -2.01 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 40 HIS 0.001 0.000 HIS A 207 PHE 0.005 0.001 PHE A 153 TYR 0.010 0.002 TYR B 146 ARG 0.003 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 ASP cc_start: 0.8196 (t0) cc_final: 0.7915 (t70) REVERT: B 217 ARG cc_start: 0.8466 (mtm180) cc_final: 0.8122 (mtm180) REVERT: C 26 MET cc_start: 0.8624 (tpp) cc_final: 0.7581 (pmm) REVERT: C 66 TRP cc_start: 0.8383 (m100) cc_final: 0.8083 (m100) REVERT: C 75 MET cc_start: 0.7701 (mmt) cc_final: 0.6664 (mmm) REVERT: C 87 ASP cc_start: 0.8337 (m-30) cc_final: 0.7357 (t0) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 0.2024 time to fit residues: 9.5383 Evaluate side-chains 31 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 24 optimal weight: 0.0670 chunk 44 optimal weight: 5.9990 chunk 13 optimal weight: 0.0570 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4205 Z= 0.227 Angle : 0.613 7.883 5714 Z= 0.311 Chirality : 0.042 0.128 657 Planarity : 0.004 0.050 727 Dihedral : 4.699 18.431 631 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.49 % Allowed : 14.29 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.34), residues: 521 helix: -0.32 (0.86), residues: 30 sheet: 0.22 (0.33), residues: 218 loop : -1.82 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 161 HIS 0.002 0.001 HIS B 204 PHE 0.007 0.001 PHE C 108 TYR 0.013 0.002 TYR B 146 ARG 0.012 0.001 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 MET cc_start: 0.8190 (tmm) cc_final: 0.7847 (tmm) REVERT: B 173 ASP cc_start: 0.8233 (t0) cc_final: 0.7947 (t70) REVERT: B 217 ARG cc_start: 0.8442 (mtm180) cc_final: 0.8068 (mtm180) REVERT: C 26 MET cc_start: 0.8728 (tpp) cc_final: 0.7871 (tpp) REVERT: C 75 MET cc_start: 0.7746 (mmt) cc_final: 0.6700 (mmm) REVERT: C 87 ASP cc_start: 0.8359 (m-30) cc_final: 0.7400 (t0) REVERT: C 97 MET cc_start: 0.9148 (tmm) cc_final: 0.8835 (tmm) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.2038 time to fit residues: 9.5372 Evaluate side-chains 32 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4205 Z= 0.165 Angle : 0.587 9.184 5714 Z= 0.292 Chirality : 0.042 0.130 657 Planarity : 0.004 0.050 727 Dihedral : 4.367 16.846 631 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.71 % Allowed : 15.78 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.35), residues: 521 helix: -0.71 (0.83), residues: 36 sheet: 0.50 (0.34), residues: 213 loop : -1.56 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 66 HIS 0.001 0.000 HIS A 207 PHE 0.006 0.001 PHE A 153 TYR 0.011 0.001 TYR B 146 ARG 0.004 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ILE cc_start: 0.8906 (mp) cc_final: 0.8640 (tp) REVERT: B 94 MET cc_start: 0.8169 (tmm) cc_final: 0.7793 (tmm) REVERT: B 173 ASP cc_start: 0.8147 (t0) cc_final: 0.7832 (t0) REVERT: B 217 ARG cc_start: 0.8480 (mtm180) cc_final: 0.8194 (mtm180) REVERT: C 26 MET cc_start: 0.8668 (tpp) cc_final: 0.7883 (tpp) REVERT: C 75 MET cc_start: 0.7768 (mmt) cc_final: 0.6723 (mmm) REVERT: C 87 ASP cc_start: 0.8307 (m-30) cc_final: 0.7378 (t0) REVERT: C 97 MET cc_start: 0.9181 (tmm) cc_final: 0.8857 (tmm) outliers start: 8 outliers final: 7 residues processed: 37 average time/residue: 0.1777 time to fit residues: 8.6200 Evaluate side-chains 34 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 0.0370 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4205 Z= 0.141 Angle : 0.568 7.748 5714 Z= 0.282 Chirality : 0.041 0.130 657 Planarity : 0.004 0.050 727 Dihedral : 4.137 15.951 631 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.92 % Allowed : 15.35 % Favored : 82.73 % 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: -0.67 (0.36), residues: 521 helix: 0.64 (1.01), residues: 30 sheet: 0.55 (0.33), residues: 223 loop : -1.49 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 66 HIS 0.001 0.000 HIS A 207 PHE 0.005 0.001 PHE A 153 TYR 0.009 0.001 TYR B 146 ARG 0.004 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ILE cc_start: 0.8911 (mp) cc_final: 0.8638 (tp) REVERT: B 94 MET cc_start: 0.8119 (tmm) cc_final: 0.7881 (tmm) REVERT: B 173 ASP cc_start: 0.8078 (t0) cc_final: 0.7748 (t0) REVERT: B 176 ASP cc_start: 0.8476 (t0) cc_final: 0.8099 (t0) REVERT: B 217 ARG cc_start: 0.8589 (mtm180) cc_final: 0.8230 (mtm180) REVERT: C 26 MET cc_start: 0.8624 (tpp) cc_final: 0.7754 (tpp) REVERT: C 75 MET cc_start: 0.7767 (mmt) cc_final: 0.6930 (mmm) REVERT: C 87 ASP cc_start: 0.8225 (m-30) cc_final: 0.7379 (t0) REVERT: C 97 MET cc_start: 0.9211 (tmm) cc_final: 0.8890 (tmm) outliers start: 9 outliers final: 7 residues processed: 39 average time/residue: 0.2172 time to fit residues: 10.9593 Evaluate side-chains 35 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4205 Z= 0.267 Angle : 0.619 7.583 5714 Z= 0.310 Chirality : 0.042 0.126 657 Planarity : 0.004 0.050 727 Dihedral : 4.520 18.313 631 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.13 % Allowed : 17.27 % Favored : 80.60 % 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: -0.75 (0.36), residues: 521 helix: -0.57 (0.85), residues: 36 sheet: 0.64 (0.34), residues: 213 loop : -1.48 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 161 HIS 0.003 0.001 HIS B 204 PHE 0.007 0.001 PHE B 122 TYR 0.010 0.001 TYR B 146 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 25 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ILE cc_start: 0.8909 (mp) cc_final: 0.8631 (tp) REVERT: B 94 MET cc_start: 0.8255 (tmm) cc_final: 0.6975 (tmm) REVERT: B 95 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8203 (pp30) REVERT: B 173 ASP cc_start: 0.8157 (t0) cc_final: 0.7825 (t0) REVERT: C 26 MET cc_start: 0.8708 (tpp) cc_final: 0.7700 (tpp) REVERT: C 75 MET cc_start: 0.7845 (mmt) cc_final: 0.7032 (mmm) REVERT: C 87 ASP cc_start: 0.8362 (m-30) cc_final: 0.7453 (t0) REVERT: C 97 MET cc_start: 0.9190 (tmm) cc_final: 0.8855 (tmm) outliers start: 10 outliers final: 7 residues processed: 35 average time/residue: 0.1178 time to fit residues: 6.0776 Evaluate side-chains 33 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 14 optimal weight: 0.6980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4205 Z= 0.162 Angle : 0.599 9.653 5714 Z= 0.295 Chirality : 0.042 0.129 657 Planarity : 0.004 0.050 727 Dihedral : 4.291 16.381 631 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.71 % Allowed : 17.91 % Favored : 80.38 % 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: -0.67 (0.36), residues: 521 helix: -0.35 (0.90), residues: 36 sheet: 0.61 (0.34), residues: 219 loop : -1.42 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 40 HIS 0.001 0.000 HIS A 207 PHE 0.007 0.001 PHE B 124 TYR 0.010 0.001 TYR B 146 ARG 0.002 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ILE cc_start: 0.8890 (mp) cc_final: 0.8622 (tp) REVERT: B 94 MET cc_start: 0.8039 (tmm) cc_final: 0.6863 (tmm) REVERT: B 173 ASP cc_start: 0.8097 (t0) cc_final: 0.7734 (t0) REVERT: B 176 ASP cc_start: 0.8460 (t0) cc_final: 0.8113 (t0) REVERT: C 26 MET cc_start: 0.8652 (tpp) cc_final: 0.7826 (tpp) REVERT: C 75 MET cc_start: 0.7821 (mmt) cc_final: 0.6918 (mmm) REVERT: C 87 ASP cc_start: 0.8246 (m-30) cc_final: 0.7383 (t0) REVERT: C 97 MET cc_start: 0.9225 (tmm) cc_final: 0.8890 (tmm) outliers start: 8 outliers final: 7 residues processed: 34 average time/residue: 0.1379 time to fit residues: 6.7877 Evaluate side-chains 32 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4205 Z= 0.298 Angle : 0.648 9.906 5714 Z= 0.325 Chirality : 0.042 0.148 657 Planarity : 0.004 0.051 727 Dihedral : 4.699 20.107 631 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.71 % Allowed : 17.70 % Favored : 80.60 % 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: -0.74 (0.36), residues: 521 helix: -0.42 (0.86), residues: 36 sheet: 0.59 (0.34), residues: 213 loop : -1.45 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 161 HIS 0.003 0.001 HIS B 204 PHE 0.006 0.001 PHE A 153 TYR 0.012 0.002 TYR B 146 ARG 0.004 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 MET cc_start: 0.8229 (tmm) cc_final: 0.7910 (tmm) REVERT: B 173 ASP cc_start: 0.8149 (t0) cc_final: 0.7810 (t0) REVERT: C 26 MET cc_start: 0.8755 (tpp) cc_final: 0.7760 (tpp) REVERT: C 75 MET cc_start: 0.7892 (mmt) cc_final: 0.7053 (mmm) REVERT: C 87 ASP cc_start: 0.8399 (m-30) cc_final: 0.7490 (t0) outliers start: 8 outliers final: 8 residues processed: 32 average time/residue: 0.1274 time to fit residues: 6.1872 Evaluate side-chains 32 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4205 Z= 0.235 Angle : 0.624 10.239 5714 Z= 0.312 Chirality : 0.042 0.150 657 Planarity : 0.004 0.051 727 Dihedral : 4.593 19.053 631 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.49 % Allowed : 18.55 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.36), residues: 521 helix: -0.36 (0.87), residues: 36 sheet: 0.67 (0.34), residues: 213 loop : -1.43 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 161 HIS 0.002 0.001 HIS B 204 PHE 0.006 0.001 PHE A 153 TYR 0.011 0.001 TYR B 146 ARG 0.004 0.000 ARG B 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 MET cc_start: 0.8211 (tmm) cc_final: 0.7888 (tmm) REVERT: B 173 ASP cc_start: 0.8136 (t0) cc_final: 0.7765 (t0) REVERT: B 176 ASP cc_start: 0.8518 (t0) cc_final: 0.8168 (t0) REVERT: C 26 MET cc_start: 0.8715 (tpp) cc_final: 0.7780 (mpp) REVERT: C 75 MET cc_start: 0.7905 (mmt) cc_final: 0.7091 (mmm) REVERT: C 87 ASP cc_start: 0.8319 (m-30) cc_final: 0.7443 (t0) outliers start: 7 outliers final: 7 residues processed: 32 average time/residue: 0.1207 time to fit residues: 5.7218 Evaluate side-chains 32 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.042160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.033949 restraints weight = 29168.626| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 6.13 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4205 Z= 0.147 Angle : 0.594 10.263 5714 Z= 0.294 Chirality : 0.042 0.144 657 Planarity : 0.004 0.050 727 Dihedral : 4.151 15.639 631 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.49 % Allowed : 18.76 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.36), residues: 521 helix: -0.16 (0.91), residues: 36 sheet: 0.75 (0.34), residues: 215 loop : -1.39 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 40 HIS 0.001 0.000 HIS A 207 PHE 0.005 0.001 PHE A 153 TYR 0.010 0.001 TYR C 107 ARG 0.002 0.000 ARG B 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1243.85 seconds wall clock time: 29 minutes 45.88 seconds (1785.88 seconds total)