Starting phenix.real_space_refine on Sun Mar 10 19:56:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4p_37268/03_2024/8w4p_37268_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4p_37268/03_2024/8w4p_37268.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4p_37268/03_2024/8w4p_37268_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4p_37268/03_2024/8w4p_37268_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4p_37268/03_2024/8w4p_37268_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4p_37268/03_2024/8w4p_37268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4p_37268/03_2024/8w4p_37268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4p_37268/03_2024/8w4p_37268_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4p_37268/03_2024/8w4p_37268_updated.pdb" } resolution = 3.48 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= 0.009 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: 5 Type Number sf(0) Gaussians Mg 30 5.21 5 S 1 5.16 5 C 3130 2.51 5 N 695 2.21 5 O 675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4531 Number of models: 1 Model: "" Number of chains: 6 Chain: "p" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1271 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 16, 'TRANS': 197} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 408 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 356 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 11, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 269 Chain: "4" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 765 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'TRANS': 152} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 153 Planarities with less than four sites: {'UNK:plan-1': 153} Unresolved non-hydrogen planarities: 153 Chain: "3" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 992 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 10, 'TRANS': 152} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 6, 'TYR%COO:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "p" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 432 Unusual residues: {'A86': 1, 'CLA': 9, 'DD6': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'CLA:plan-2': 2, 'CLA:plan-3': 6, 'CLA:plan-4': 9, 'CLA:plan-5': 9} Unresolved non-hydrogen planarities: 95 Chain: "4" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 516 Unusual residues: {'A86': 3, 'CLA': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'CLA:plan-2': 4, 'CLA:plan-3': 8, 'CLA:plan-4': 10, 'CLA:plan-5': 10} Unresolved non-hydrogen planarities: 113 Chain: "3" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 555 Unusual residues: {'A86': 2, 'CLA': 11, 'DD6': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-3': 7, 'CLA:plan-4': 10, 'CLA:plan-5': 11, 'CLA:plan-6': 1} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 3.35, per 1000 atoms: 0.74 Number of scatterers: 4531 At special positions: 0 Unit cell: (118.72, 113.42, 73.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 1 16.00 Mg 30 11.99 O 675 8.00 N 695 7.00 C 3130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 597.6 milliseconds 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 0 sheets defined 70.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'p' and resid 84 through 107 removed outlier: 3.622A pdb=" N LEU p 104 " --> pdb=" O GLN p 100 " (cutoff:3.500A) Processing helix chain 'p' and resid 132 through 138 Processing helix chain 'p' and resid 141 through 164 removed outlier: 3.845A pdb=" N GLU p 164 " --> pdb=" O ILE p 160 " (cutoff:3.500A) Processing helix chain 'p' and resid 170 through 172 No H-bonds generated for 'chain 'p' and resid 170 through 172' Processing helix chain 'p' and resid 191 through 220 removed outlier: 3.795A pdb=" N PHE p 213 " --> pdb=" O MET p 209 " (cutoff:3.500A) Processing helix chain 'p' and resid 226 through 233 Proline residue: p 232 - end of helix Processing helix chain '4' and resid 20 through 23 Processing helix chain '4' and resid 26 through 52 removed outlier: 3.753A pdb=" N UNK 4 42 " --> pdb=" O UNK 4 38 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N UNK 4 45 " --> pdb=" O UNK 4 41 " (cutoff:3.500A) Processing helix chain '4' and resid 85 through 104 removed outlier: 4.145A pdb=" N UNK 4 89 " --> pdb=" O UNK 4 85 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N UNK 4 103 " --> pdb=" O UNK 4 99 " (cutoff:3.500A) Processing helix chain '4' and resid 130 through 159 removed outlier: 4.273A pdb=" N UNK 4 137 " --> pdb=" O UNK 4 133 " (cutoff:3.500A) Processing helix chain '3' and resid 59 through 85 Proline residue: 3 83 - end of helix Processing helix chain '3' and resid 99 through 101 No H-bonds generated for 'chain '3' and resid 99 through 101' Processing helix chain '3' and resid 105 through 111 removed outlier: 3.563A pdb=" N ALA 3 108 " --> pdb=" O GLY 3 105 " (cutoff:3.500A) Processing helix chain '3' and resid 114 through 130 Processing helix chain '3' and resid 144 through 177 removed outlier: 3.603A pdb=" N LEU 3 163 " --> pdb=" O ARG 3 159 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 570 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: 0.97 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 1437 1.37 - 1.55: 3208 1.55 - 1.73: 53 1.73 - 1.91: 1 1.91 - 2.09: 120 Bond restraints: 4819 Sorted by residual: bond pdb=" C27 DD6 3 303 " pdb=" C29 DD6 3 303 " ideal model delta sigma weight residual 1.545 1.256 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C30 DD6 p 611 " pdb=" C31 DD6 p 611 " ideal model delta sigma weight residual 1.545 1.258 0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C27 DD6 p 611 " pdb=" C29 DD6 p 611 " ideal model delta sigma weight residual 1.545 1.258 0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C30 DD6 3 303 " pdb=" C31 DD6 3 303 " ideal model delta sigma weight residual 1.545 1.261 0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C31 DD6 3 303 " pdb=" C36 DD6 3 303 " ideal model delta sigma weight residual 1.612 1.330 0.282 2.00e-02 2.50e+03 1.98e+02 ... (remaining 4814 not shown) Histogram of bond angle deviations from ideal: 55.62 - 80.49: 24 80.49 - 105.36: 288 105.36 - 130.23: 6656 130.23 - 155.10: 156 155.10 - 179.97: 70 Bond angle restraints: 7194 Sorted by residual: angle pdb=" C28 DD6 3 303 " pdb=" C27 DD6 3 303 " pdb=" C29 DD6 3 303 " ideal model delta sigma weight residual 68.18 120.60 -52.42 3.00e+00 1.11e-01 3.05e+02 angle pdb=" C28 DD6 p 611 " pdb=" C27 DD6 p 611 " pdb=" C29 DD6 p 611 " ideal model delta sigma weight residual 68.18 119.28 -51.10 3.00e+00 1.11e-01 2.90e+02 angle pdb=" C16 DD6 3 303 " pdb=" C15 DD6 3 303 " pdb=" O1 DD6 3 303 " ideal model delta sigma weight residual 153.95 106.85 47.10 3.00e+00 1.11e-01 2.47e+02 angle pdb=" C DD6 3 303 " pdb=" C1 DD6 3 303 " pdb=" C24 DD6 3 303 " ideal model delta sigma weight residual 74.49 120.57 -46.08 3.00e+00 1.11e-01 2.36e+02 angle pdb=" C DD6 p 611 " pdb=" C1 DD6 p 611 " pdb=" C24 DD6 p 611 " ideal model delta sigma weight residual 74.49 118.95 -44.46 3.00e+00 1.11e-01 2.20e+02 ... (remaining 7189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 2024 35.29 - 70.58: 73 70.58 - 105.86: 20 105.86 - 141.15: 4 141.15 - 176.44: 5 Dihedral angle restraints: 2126 sinusoidal: 617 harmonic: 1509 Sorted by residual: dihedral pdb=" C34 A86 4 202 " pdb=" C38 A86 4 202 " pdb=" O4 A86 4 202 " pdb=" C39 A86 4 202 " ideal model delta sinusoidal sigma weight residual -177.27 -0.83 -176.44 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C15 DD6 3 303 " pdb=" C20 DD6 3 303 " pdb=" O1 DD6 3 303 " pdb=" C19 DD6 3 303 " ideal model delta sinusoidal sigma weight residual 79.23 -110.78 -169.99 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C15 DD6 p 611 " pdb=" C20 DD6 p 611 " pdb=" O1 DD6 p 611 " pdb=" C19 DD6 p 611 " ideal model delta sinusoidal sigma weight residual 79.23 -111.11 -169.66 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 2123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.440: 644 0.440 - 0.880: 2 0.880 - 1.320: 1 1.320 - 1.760: 2 1.760 - 2.201: 2 Chirality restraints: 651 Sorted by residual: chirality pdb=" C15 DD6 3 303 " pdb=" C14 DD6 3 303 " pdb=" C16 DD6 3 303 " pdb=" O1 DD6 3 303 " both_signs ideal model delta sigma weight residual True 0.11 -2.31 -2.20 2.00e-01 2.50e+01 1.21e+02 chirality pdb=" C20 DD6 3 303 " pdb=" C15 DD6 3 303 " pdb=" C19 DD6 3 303 " pdb=" C21 DD6 3 303 " both_signs ideal model delta sigma weight residual True 2.74 0.92 1.82 2.00e-01 2.50e+01 8.27e+01 chirality pdb=" C20 DD6 p 611 " pdb=" C15 DD6 p 611 " pdb=" C19 DD6 p 611 " pdb=" C21 DD6 p 611 " both_signs ideal model delta sigma weight residual True 2.74 1.00 1.73 2.00e-01 2.50e+01 7.51e+01 ... (remaining 648 not shown) Planarity restraints: 1033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 A86 p 610 " 0.006 2.00e-02 2.50e+03 6.20e-02 3.85e+01 pdb=" C29 A86 p 610 " -0.058 2.00e-02 2.50e+03 pdb=" C30 A86 p 610 " 0.099 2.00e-02 2.50e+03 pdb=" C31 A86 p 610 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA 3 82 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO 3 83 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO 3 83 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO 3 83 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER p 231 " -0.064 5.00e-02 4.00e+02 9.73e-02 1.51e+01 pdb=" N PRO p 232 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO p 232 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO p 232 " -0.054 5.00e-02 4.00e+02 ... (remaining 1030 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1078 2.83 - 3.34: 4481 3.34 - 3.86: 7627 3.86 - 4.38: 7343 4.38 - 4.90: 11550 Nonbonded interactions: 32079 Sorted by model distance: nonbonded pdb=" C2B CLA p 604 " pdb=" C37 DD6 p 611 " model vdw 2.306 3.680 nonbonded pdb=" O ARG p 161 " pdb=" N GLN p 165 " model vdw 2.341 2.520 nonbonded pdb=" CMB CLA p 604 " pdb=" C37 DD6 p 611 " model vdw 2.353 3.880 nonbonded pdb=" NE2 GLN p 200 " pdb=" OBD CLA p 607 " model vdw 2.366 2.520 nonbonded pdb=" O UNK 4 70 " pdb=" N UNK 4 73 " model vdw 2.403 2.520 ... (remaining 32074 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=0.50 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: 5.610 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: 27.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.500 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.017 0.289 4819 Z= 0.869 Angle : 2.886 52.421 7194 Z= 1.032 Chirality : 0.169 2.201 651 Planarity : 0.009 0.107 1033 Dihedral : 23.393 176.439 1148 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.80 % Allowed : 15.28 % Favored : 83.91 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.40), residues: 373 helix: -0.45 (0.35), residues: 175 sheet: None (None), residues: 0 loop : -4.07 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP p 153 HIS 0.006 0.003 HIS p 95 PHE 0.016 0.002 PHE p 213 TYR 0.008 0.001 TYR 3 80 ARG 0.010 0.001 ARG 3 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.340 Fit side-chains REVERT: p 84 ASP cc_start: 0.8634 (p0) cc_final: 0.8299 (p0) REVERT: 3 172 ASP cc_start: 0.8809 (t0) cc_final: 0.8443 (t0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0955 time to fit residues: 4.7363 Evaluate side-chains 26 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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: 0.9980 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4819 Z= 0.251 Angle : 1.298 25.443 7194 Z= 0.476 Chirality : 0.096 0.945 651 Planarity : 0.005 0.076 1033 Dihedral : 22.933 178.481 885 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.53 % Favored : 88.20 % Rotamer: Outliers : 2.40 % Allowed : 13.60 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.43), residues: 373 helix: 1.11 (0.36), residues: 175 sheet: None (None), residues: 0 loop : -3.61 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP p 153 HIS 0.007 0.003 HIS 3 171 PHE 0.007 0.001 PHE p 58 TYR 0.005 0.001 TYR 3 80 ARG 0.006 0.001 ARG 3 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.296 Fit side-chains REVERT: p 84 ASP cc_start: 0.8785 (p0) cc_final: 0.8394 (p0) REVERT: 3 80 TYR cc_start: 0.9331 (OUTLIER) cc_final: 0.8326 (t80) REVERT: 3 172 ASP cc_start: 0.8633 (t0) cc_final: 0.8333 (t0) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.0825 time to fit residues: 3.9702 Evaluate side-chains 28 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 246 PHE Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 13 optimal weight: 0.0060 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 118 ASN ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4819 Z= 0.224 Angle : 1.226 24.675 7194 Z= 0.447 Chirality : 0.091 0.897 651 Planarity : 0.005 0.067 1033 Dihedral : 21.673 177.029 885 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.33 % Favored : 87.40 % Rotamer: Outliers : 4.80 % Allowed : 14.40 % Favored : 80.80 % 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: -0.86 (0.45), residues: 373 helix: 1.93 (0.37), residues: 173 sheet: None (None), residues: 0 loop : -3.13 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP p 153 HIS 0.007 0.004 HIS p 95 PHE 0.007 0.001 PHE p 106 TYR 0.003 0.000 TYR p 245 ARG 0.001 0.000 ARG 3 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.329 Fit side-chains REVERT: p 84 ASP cc_start: 0.8919 (p0) cc_final: 0.8478 (p0) REVERT: 3 80 TYR cc_start: 0.9329 (OUTLIER) cc_final: 0.8412 (t80) REVERT: 3 124 VAL cc_start: 0.8672 (t) cc_final: 0.8454 (p) REVERT: 3 172 ASP cc_start: 0.8691 (t0) cc_final: 0.8341 (t0) outliers start: 6 outliers final: 4 residues processed: 32 average time/residue: 0.0808 time to fit residues: 4.1699 Evaluate side-chains 31 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 224 THR Chi-restraints excluded: chain p residue 246 PHE Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 0.0040 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4819 Z= 0.322 Angle : 1.259 23.006 7194 Z= 0.469 Chirality : 0.092 0.915 651 Planarity : 0.005 0.062 1033 Dihedral : 20.622 175.739 885 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.26 % Favored : 88.47 % Rotamer: Outliers : 6.40 % Allowed : 14.40 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.45), residues: 373 helix: 1.75 (0.37), residues: 175 sheet: None (None), residues: 0 loop : -3.05 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP p 87 HIS 0.007 0.004 HIS p 95 PHE 0.015 0.002 PHE p 216 TYR 0.008 0.001 TYR p 245 ARG 0.003 0.001 ARG 3 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.335 Fit side-chains REVERT: p 84 ASP cc_start: 0.9024 (p0) cc_final: 0.8633 (p0) REVERT: 3 80 TYR cc_start: 0.9325 (OUTLIER) cc_final: 0.8538 (t80) REVERT: 3 172 ASP cc_start: 0.8692 (t0) cc_final: 0.8167 (t0) outliers start: 8 outliers final: 4 residues processed: 32 average time/residue: 0.0811 time to fit residues: 4.2086 Evaluate side-chains 28 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 224 THR Chi-restraints excluded: chain p residue 246 PHE Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 171 HIS ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 4819 Z= 0.428 Angle : 1.313 22.290 7194 Z= 0.495 Chirality : 0.092 0.908 651 Planarity : 0.006 0.056 1033 Dihedral : 19.828 175.172 885 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.14 % Favored : 86.60 % Rotamer: Outliers : 7.20 % Allowed : 16.00 % Favored : 76.80 % 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: -1.17 (0.44), residues: 373 helix: 1.39 (0.37), residues: 170 sheet: None (None), residues: 0 loop : -2.91 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP p 87 HIS 0.009 0.004 HIS 3 171 PHE 0.013 0.002 PHE p 216 TYR 0.009 0.001 TYR p 245 ARG 0.003 0.001 ARG 3 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 22 time to evaluate : 0.355 Fit side-chains REVERT: p 84 ASP cc_start: 0.9123 (p0) cc_final: 0.8744 (p0) REVERT: 3 80 TYR cc_start: 0.9268 (OUTLIER) cc_final: 0.8581 (t80) REVERT: 3 172 ASP cc_start: 0.8682 (t0) cc_final: 0.8132 (t0) outliers start: 9 outliers final: 6 residues processed: 28 average time/residue: 0.0917 time to fit residues: 4.2437 Evaluate side-chains 29 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 22 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 65 THR Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 220 LEU Chi-restraints excluded: chain p residue 224 THR Chi-restraints excluded: chain p residue 246 PHE Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 218 GLN ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4819 Z= 0.234 Angle : 1.175 21.979 7194 Z= 0.430 Chirality : 0.091 0.930 651 Planarity : 0.004 0.058 1033 Dihedral : 18.915 175.864 885 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.72 % Favored : 89.01 % Rotamer: Outliers : 3.20 % Allowed : 21.60 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.46), residues: 373 helix: 1.82 (0.37), residues: 177 sheet: None (None), residues: 0 loop : -2.79 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP p 87 HIS 0.006 0.002 HIS p 95 PHE 0.006 0.001 PHE p 246 TYR 0.004 0.001 TYR p 194 ARG 0.003 0.001 ARG 3 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.329 Fit side-chains REVERT: p 84 ASP cc_start: 0.9111 (p0) cc_final: 0.8731 (p0) REVERT: 3 80 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8507 (t80) REVERT: 3 172 ASP cc_start: 0.8649 (t0) cc_final: 0.8166 (t0) outliers start: 4 outliers final: 1 residues processed: 27 average time/residue: 0.0912 time to fit residues: 3.9743 Evaluate side-chains 24 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 4819 Z= 0.523 Angle : 1.313 23.145 7194 Z= 0.503 Chirality : 0.093 0.909 651 Planarity : 0.006 0.053 1033 Dihedral : 18.960 175.760 885 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.67 % Favored : 86.06 % Rotamer: Outliers : 5.60 % Allowed : 20.80 % Favored : 73.60 % 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: -1.23 (0.45), residues: 373 helix: 1.18 (0.36), residues: 175 sheet: None (None), residues: 0 loop : -2.88 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP p 87 HIS 0.009 0.004 HIS 3 157 PHE 0.015 0.002 PHE p 216 TYR 0.013 0.001 TYR p 245 ARG 0.003 0.001 ARG 3 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.345 Fit side-chains REVERT: p 84 ASP cc_start: 0.9178 (p0) cc_final: 0.8854 (p0) REVERT: 3 80 TYR cc_start: 0.9368 (OUTLIER) cc_final: 0.8719 (t80) REVERT: 3 172 ASP cc_start: 0.8834 (t0) cc_final: 0.8292 (t0) outliers start: 7 outliers final: 5 residues processed: 25 average time/residue: 0.0808 time to fit residues: 3.3990 Evaluate side-chains 26 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 220 LEU Chi-restraints excluded: chain p residue 224 THR Chi-restraints excluded: chain p residue 246 PHE Chi-restraints excluded: chain 3 residue 77 VAL Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4819 Z= 0.231 Angle : 1.090 23.597 7194 Z= 0.405 Chirality : 0.091 0.930 651 Planarity : 0.004 0.058 1033 Dihedral : 18.230 176.125 885 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.46 % Favored : 89.28 % Rotamer: Outliers : 4.00 % Allowed : 22.40 % Favored : 73.60 % 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: -0.62 (0.46), residues: 373 helix: 1.78 (0.37), residues: 176 sheet: None (None), residues: 0 loop : -2.68 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP p 87 HIS 0.006 0.003 HIS p 95 PHE 0.007 0.001 PHE p 246 TYR 0.004 0.000 TYR p 194 ARG 0.001 0.000 ARG 3 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.307 Fit side-chains REVERT: p 84 ASP cc_start: 0.9138 (p0) cc_final: 0.8797 (p0) REVERT: 3 80 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.8500 (t80) REVERT: 3 172 ASP cc_start: 0.8717 (t0) cc_final: 0.8230 (t0) outliers start: 5 outliers final: 2 residues processed: 25 average time/residue: 0.0811 time to fit residues: 3.4043 Evaluate side-chains 26 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain 3 residue 77 VAL Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 51 optimal weight: 0.0270 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 4819 Z= 0.403 Angle : 1.193 23.578 7194 Z= 0.454 Chirality : 0.093 0.926 651 Planarity : 0.006 0.054 1033 Dihedral : 18.348 176.024 885 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.67 % Favored : 86.06 % Rotamer: Outliers : 6.40 % Allowed : 20.00 % Favored : 73.60 % 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: -0.87 (0.45), residues: 373 helix: 1.57 (0.37), residues: 169 sheet: None (None), residues: 0 loop : -2.66 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP p 87 HIS 0.007 0.003 HIS p 95 PHE 0.013 0.002 PHE p 216 TYR 0.009 0.001 TYR p 245 ARG 0.003 0.001 ARG p 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 22 time to evaluate : 0.306 Fit side-chains REVERT: p 84 ASP cc_start: 0.9179 (p0) cc_final: 0.8870 (p0) REVERT: 3 80 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.8654 (t80) REVERT: 3 172 ASP cc_start: 0.8837 (t0) cc_final: 0.8268 (t0) outliers start: 8 outliers final: 6 residues processed: 28 average time/residue: 0.0790 time to fit residues: 3.7008 Evaluate side-chains 28 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 21 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 205 CYS Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 224 THR Chi-restraints excluded: chain p residue 246 PHE Chi-restraints excluded: chain 3 residue 77 VAL Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4819 Z= 0.230 Angle : 1.081 22.947 7194 Z= 0.401 Chirality : 0.091 0.934 651 Planarity : 0.004 0.057 1033 Dihedral : 17.958 175.944 885 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.53 % Favored : 88.20 % Rotamer: Outliers : 4.00 % Allowed : 23.20 % Favored : 72.80 % 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: -0.41 (0.46), residues: 373 helix: 2.03 (0.37), residues: 170 sheet: None (None), residues: 0 loop : -2.51 (0.47), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP p 87 HIS 0.006 0.003 HIS p 95 PHE 0.008 0.001 PHE p 246 TYR 0.004 0.000 TYR p 194 ARG 0.001 0.000 ARG 3 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 24 time to evaluate : 0.294 Fit side-chains REVERT: p 84 ASP cc_start: 0.9174 (p0) cc_final: 0.8834 (p0) REVERT: 3 80 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8544 (t80) REVERT: 3 172 ASP cc_start: 0.8791 (t0) cc_final: 0.8283 (t0) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.0765 time to fit residues: 3.4796 Evaluate side-chains 27 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 205 CYS Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain 3 residue 77 VAL Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 174 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 = 0.3382 r_free = 0.3382 target = 0.053162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.046551 restraints weight = 37146.144| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 4.69 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4819 Z= 0.326 Angle : 1.133 23.399 7194 Z= 0.426 Chirality : 0.092 0.918 651 Planarity : 0.005 0.055 1033 Dihedral : 17.972 175.900 885 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.67 % Favored : 86.06 % Rotamer: Outliers : 4.80 % Allowed : 23.20 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.47), residues: 373 helix: 1.93 (0.37), residues: 170 sheet: None (None), residues: 0 loop : -2.48 (0.48), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP p 87 HIS 0.007 0.003 HIS p 95 PHE 0.010 0.001 PHE p 216 TYR 0.005 0.001 TYR 3 80 ARG 0.002 0.001 ARG p 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1195.68 seconds wall clock time: 22 minutes 9.50 seconds (1329.50 seconds total)