Starting phenix.real_space_refine on Mon Jun 24 18:31:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs3_38613/06_2024/8xs3_38613.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs3_38613/06_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_38613/06_2024/8xs3_38613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs3_38613/06_2024/8xs3_38613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs3_38613/06_2024/8xs3_38613.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs3_38613/06_2024/8xs3_38613.pdb" } 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 Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "B TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "C TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 3.67, per 1000 atoms: 0.89 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 - 3.50 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 D 1 " - " NAG D 2 " NAG-ASN " NAG C 301 " - " ASN C 94 " " NAG D 1 " - " ASN C 120 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 758.2 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: 0.54 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: 1.09 Time building geometry restraints manager: 1.85 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: 100.20 - 106.96: 145 106.96 - 113.72: 2422 113.72 - 120.49: 1410 120.49 - 127.25: 1690 127.25 - 134.01: 47 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 2.520 nonbonded pdb=" OE1 GLU B 39 " pdb=" OH TYR B 41 " model vdw 2.178 2.440 nonbonded pdb=" O HIS A 171 " pdb=" OG SER A 187 " model vdw 2.201 2.440 nonbonded pdb=" NZ LYS A 216 " pdb=" O ARG A 217 " model vdw 2.203 2.520 nonbonded pdb=" NH1 ARG A 98 " pdb=" O ARG A 99 " model vdw 2.213 2.520 ... (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 ========== 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: 2.400 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: 9.230 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.970 Find NCS groups from input model: 0.120 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.730 ------------------------------------------------------------------------------- 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 : 0.488 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: 0.2370 time to fit residues: 12.4016 Evaluate side-chains 30 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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: 10.0000 chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.8286 moved from start: 0.1256 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= 0.208 Angle : 0.620 6.475 5714 Z= 0.316 Chirality : 0.043 0.136 657 Planarity : 0.004 0.049 727 Dihedral : 5.759 40.433 631 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.07 % Allowed : 11.51 % Favored : 87.42 % 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: -2.09 (0.33), residues: 521 helix: -1.95 (0.69), residues: 29 sheet: -0.32 (0.33), residues: 214 loop : -2.27 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 66 HIS 0.001 0.000 HIS B 195 PHE 0.008 0.001 PHE A 153 TYR 0.013 0.002 TYR C 107 ARG 0.003 0.000 ARG B 148 *********************** 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 38 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 ARG cc_start: 0.8533 (mtm180) cc_final: 0.8167 (mtm180) REVERT: C 26 MET cc_start: 0.8646 (tpp) cc_final: 0.7856 (pmm) REVERT: C 75 MET cc_start: 0.7668 (mmt) cc_final: 0.6595 (mmm) outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.2058 time to fit residues: 9.8766 Evaluate side-chains 27 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain C residue 27 ASN 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: 4.9990 chunk 13 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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: 0.8321 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4205 Z= 0.270 Angle : 0.617 6.488 5714 Z= 0.316 Chirality : 0.042 0.127 657 Planarity : 0.004 0.048 727 Dihedral : 5.316 31.758 631 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.13 % Allowed : 13.86 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.34), residues: 521 helix: -1.51 (0.75), residues: 30 sheet: -0.07 (0.33), residues: 213 loop : -2.07 (0.34), residues: 278 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 0.008 0.001 PHE C 108 TYR 0.012 0.002 TYR B 146 ARG 0.003 0.000 ARG B 148 *********************** 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 36 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 26 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 ARG cc_start: 0.8486 (mtm180) cc_final: 0.8172 (mtm180) REVERT: C 26 MET cc_start: 0.8831 (tpp) cc_final: 0.8070 (tpp) REVERT: C 75 MET cc_start: 0.7708 (mmt) cc_final: 0.6648 (mmm) REVERT: C 97 MET cc_start: 0.9230 (tmm) cc_final: 0.8907 (tmm) outliers start: 10 outliers final: 7 residues processed: 35 average time/residue: 0.1613 time to fit residues: 7.5572 Evaluate side-chains 30 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 27 ASN Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.0370 chunk 22 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 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: 0.8387 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 4205 Z= 0.506 Angle : 0.783 7.201 5714 Z= 0.398 Chirality : 0.045 0.145 657 Planarity : 0.005 0.051 727 Dihedral : 5.964 28.250 631 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.41 % Allowed : 15.57 % Favored : 81.02 % 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: -1.86 (0.34), residues: 521 helix: -2.02 (0.72), residues: 30 sheet: -0.09 (0.33), residues: 215 loop : -2.17 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 161 HIS 0.004 0.001 HIS B 204 PHE 0.011 0.002 PHE C 108 TYR 0.016 0.002 TYR B 146 ARG 0.004 0.001 ARG B 82 *********************** 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 38 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 22 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 MET cc_start: 0.8965 (tpp) cc_final: 0.8180 (mpp) REVERT: C 75 MET cc_start: 0.7868 (mmt) cc_final: 0.7054 (mmm) REVERT: C 97 MET cc_start: 0.9180 (tmm) cc_final: 0.8822 (tmm) outliers start: 16 outliers final: 14 residues processed: 36 average time/residue: 0.1332 time to fit residues: 6.7480 Evaluate side-chains 36 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 22 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 46 GLU 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 87 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 87 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: 4.9990 chunk 20 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4205 Z= 0.296 Angle : 0.638 7.088 5714 Z= 0.325 Chirality : 0.043 0.131 657 Planarity : 0.004 0.050 727 Dihedral : 5.437 25.560 631 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.41 % Allowed : 17.70 % Favored : 78.89 % 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: -1.64 (0.34), residues: 521 helix: -1.52 (0.76), residues: 30 sheet: -0.02 (0.33), residues: 218 loop : -2.01 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 40 HIS 0.002 0.001 HIS B 204 PHE 0.007 0.001 PHE A 153 TYR 0.014 0.002 TYR B 146 ARG 0.002 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 41 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 25 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 MET cc_start: 0.8903 (tpp) cc_final: 0.8342 (tpp) REVERT: C 75 MET cc_start: 0.7850 (mmt) cc_final: 0.7050 (mmm) REVERT: C 97 MET cc_start: 0.9200 (tmm) cc_final: 0.8862 (tmm) outliers start: 16 outliers final: 11 residues processed: 40 average time/residue: 0.1344 time to fit residues: 7.5032 Evaluate side-chains 33 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 22 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 46 GLU 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 30 LYS 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: 2.9990 chunk 50 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.8319 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4205 Z= 0.206 Angle : 0.603 7.402 5714 Z= 0.306 Chirality : 0.043 0.160 657 Planarity : 0.004 0.049 727 Dihedral : 4.943 19.120 631 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.77 % Allowed : 18.55 % Favored : 78.68 % 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: -1.35 (0.35), residues: 521 helix: -0.90 (0.83), residues: 30 sheet: 0.11 (0.34), residues: 221 loop : -1.82 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 40 HIS 0.001 0.001 HIS A 207 PHE 0.006 0.001 PHE A 153 TYR 0.013 0.002 TYR B 192 ARG 0.002 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 40 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 27 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 MET cc_start: 0.8829 (tpp) cc_final: 0.8246 (tpp) REVERT: C 75 MET cc_start: 0.7853 (mmt) cc_final: 0.6965 (mmm) REVERT: C 97 MET cc_start: 0.9229 (tmm) cc_final: 0.8898 (tmm) outliers start: 13 outliers final: 9 residues processed: 40 average time/residue: 0.1243 time to fit residues: 7.0165 Evaluate side-chains 32 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 23 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 20 VAL 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: 8.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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: 0.8337 moved from start: 0.2176 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= 0.284 Angle : 0.646 7.537 5714 Z= 0.323 Chirality : 0.043 0.146 657 Planarity : 0.004 0.050 727 Dihedral : 5.016 18.537 631 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.62 % Allowed : 18.12 % Favored : 78.25 % 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: -1.28 (0.35), residues: 521 helix: -0.67 (0.83), residues: 30 sheet: 0.17 (0.34), residues: 221 loop : -1.80 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 66 HIS 0.003 0.001 HIS B 204 PHE 0.006 0.001 PHE B 124 TYR 0.013 0.002 TYR B 146 ARG 0.002 0.000 ARG A 87 *********************** 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 39 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 22 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 26 MET cc_start: 0.8889 (tpp) cc_final: 0.8157 (mpp) REVERT: C 75 MET cc_start: 0.7842 (mmt) cc_final: 0.7042 (mmm) REVERT: C 97 MET cc_start: 0.9217 (tmm) cc_final: 0.8877 (tmm) outliers start: 17 outliers final: 15 residues processed: 37 average time/residue: 0.1136 time to fit residues: 6.1387 Evaluate side-chains 36 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 21 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 87 ASP 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 87 ASP Chi-restraints excluded: chain C residue 100 SER 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: 0.0060 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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: 0.8261 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4205 Z= 0.149 Angle : 0.610 9.914 5714 Z= 0.302 Chirality : 0.043 0.146 657 Planarity : 0.004 0.049 727 Dihedral : 4.468 15.795 631 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.13 % Allowed : 20.04 % Favored : 77.83 % 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: -0.84 (0.36), residues: 521 helix: 0.55 (1.00), residues: 30 sheet: 0.57 (0.34), residues: 216 loop : -1.71 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 66 HIS 0.001 0.000 HIS A 171 PHE 0.006 0.001 PHE A 153 TYR 0.010 0.001 TYR A 95 ARG 0.002 0.000 ARG B 114 *********************** 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 37 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 27 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 MET cc_start: 0.8723 (tpp) cc_final: 0.7877 (pmm) REVERT: C 27 ASN cc_start: 0.9519 (OUTLIER) cc_final: 0.9139 (p0) REVERT: C 67 LYS cc_start: 0.9228 (tptt) cc_final: 0.9022 (ptmm) REVERT: C 75 MET cc_start: 0.7859 (mmt) cc_final: 0.7019 (mmm) REVERT: C 91 TYR cc_start: 0.8040 (m-80) cc_final: 0.7622 (m-10) REVERT: C 97 MET cc_start: 0.9240 (tmm) cc_final: 0.8905 (tmm) outliers start: 10 outliers final: 8 residues processed: 37 average time/residue: 0.1323 time to fit residues: 6.9179 Evaluate side-chains 34 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 46 GLU 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 27 ASN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 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: 0.8271 moved from start: 0.2560 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= 0.163 Angle : 0.609 10.002 5714 Z= 0.304 Chirality : 0.042 0.144 657 Planarity : 0.004 0.050 727 Dihedral : 4.366 16.832 631 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.56 % Allowed : 19.83 % Favored : 77.61 % 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: -0.64 (0.36), residues: 521 helix: 0.93 (1.03), residues: 30 sheet: 0.71 (0.34), residues: 216 loop : -1.60 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 66 HIS 0.001 0.000 HIS B 204 PHE 0.004 0.001 PHE A 153 TYR 0.011 0.001 TYR B 146 ARG 0.002 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 38 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 26 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 MET cc_start: 0.8758 (tpp) cc_final: 0.7915 (tpp) REVERT: C 27 ASN cc_start: 0.9530 (OUTLIER) cc_final: 0.9206 (p0) REVERT: C 75 MET cc_start: 0.7855 (mmt) cc_final: 0.7005 (mmm) REVERT: C 97 MET cc_start: 0.9218 (tmm) cc_final: 0.8871 (tmm) outliers start: 12 outliers final: 11 residues processed: 38 average time/residue: 0.1254 time to fit residues: 6.7700 Evaluate side-chains 37 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 25 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 27 ASN 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: 6.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 4205 Z= 0.422 Angle : 0.744 9.781 5714 Z= 0.374 Chirality : 0.045 0.172 657 Planarity : 0.005 0.052 727 Dihedral : 5.186 21.670 631 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.20 % Allowed : 20.04 % Favored : 76.76 % 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: -0.95 (0.35), residues: 521 helix: 0.11 (0.86), residues: 30 sheet: 0.43 (0.34), residues: 216 loop : -1.66 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 66 HIS 0.004 0.001 HIS B 204 PHE 0.008 0.002 PHE B 122 TYR 0.016 0.002 TYR B 146 ARG 0.004 0.001 ARG B 82 ********************** 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 38 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 23 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 26 MET cc_start: 0.8913 (tpp) cc_final: 0.7711 (pmm) REVERT: C 27 ASN cc_start: 0.9534 (OUTLIER) cc_final: 0.9083 (p0) REVERT: C 75 MET cc_start: 0.7889 (mmt) cc_final: 0.7060 (mmm) REVERT: C 97 MET cc_start: 0.9195 (tmm) cc_final: 0.8853 (tmm) outliers start: 15 outliers final: 12 residues processed: 38 average time/residue: 0.1235 time to fit residues: 6.9439 Evaluate side-chains 36 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 23 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 93 VAL 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: 3.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.041259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.033695 restraints weight = 29263.389| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 5.67 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4205 Z= 0.158 Angle : 0.619 10.293 5714 Z= 0.306 Chirality : 0.043 0.156 657 Planarity : 0.004 0.049 727 Dihedral : 4.443 16.545 631 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.20 % Allowed : 20.04 % Favored : 76.76 % 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: -0.63 (0.36), residues: 521 helix: 1.03 (1.01), residues: 30 sheet: 0.73 (0.34), residues: 211 loop : -1.58 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 66 HIS 0.001 0.000 HIS B 204 PHE 0.005 0.001 PHE B 124 TYR 0.012 0.001 TYR B 146 ARG 0.001 0.000 ARG B 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1190.76 seconds wall clock time: 22 minutes 48.80 seconds (1368.80 seconds total)