Starting phenix.real_space_refine on Sun Mar 10 16:30:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcv_38256/03_2024/8xcv_38256_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcv_38256/03_2024/8xcv_38256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcv_38256/03_2024/8xcv_38256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcv_38256/03_2024/8xcv_38256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcv_38256/03_2024/8xcv_38256_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcv_38256/03_2024/8xcv_38256_neut_updated.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 P 3 5.49 5 S 14 5.16 5 C 2101 2.51 5 N 564 2.21 5 O 628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A ASP 133": "OD1" <-> "OD2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3310 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3272 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 415, 3253 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 394} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 415, 3253 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 394} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 3303 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 38 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1, 'water': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 4.03, per 1000 atoms: 1.22 Number of scatterers: 3310 At special positions: 0 Unit cell: (66.928, 72.944, 72.944, 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 14 16.00 P 3 15.00 O 628 8.00 N 564 7.00 C 2101 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=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 1.4 seconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 4 sheets defined 49.2% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.793A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.713A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.662A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 303 through 308 removed outlier: 4.610A pdb=" N ASP A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 366 through 391 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.706A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 68 through 71 Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.285A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.847A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 164 hydrogen bonds defined for protein. 475 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: 0.88 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1064 1.34 - 1.46: 606 1.46 - 1.57: 1682 1.57 - 1.69: 3 1.69 - 1.81: 27 Bond restraints: 3382 Sorted by residual: bond pdb=" C TRP A 89 " pdb=" CA BTRP A 89 " ideal model delta sigma weight residual 1.522 1.642 -0.119 1.39e-02 5.18e+03 7.39e+01 bond pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " ideal model delta sigma weight residual 1.736 1.569 0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" N ARG A 370 " pdb=" CA BARG A 370 " ideal model delta sigma weight residual 1.457 1.551 -0.095 1.33e-02 5.65e+03 5.07e+01 bond pdb=" C4A NAP A 500 " pdb=" N3A NAP A 500 " ideal model delta sigma weight residual 1.332 1.440 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C6A NAP A 500 " pdb=" N6A NAP A 500 " ideal model delta sigma weight residual 1.335 1.435 -0.100 2.00e-02 2.50e+03 2.49e+01 ... (remaining 3377 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.59: 113 106.59 - 113.45: 1847 113.45 - 120.32: 1209 120.32 - 127.19: 1374 127.19 - 134.06: 54 Bond angle restraints: 4597 Sorted by residual: angle pdb=" N THR A 88 " pdb=" CA THR A 88 " pdb=" C THR A 88 " ideal model delta sigma weight residual 111.28 105.80 5.48 1.09e+00 8.42e-01 2.53e+01 angle pdb=" N MET A 90 " pdb=" CA MET A 90 " pdb=" C MET A 90 " ideal model delta sigma weight residual 111.69 105.67 6.02 1.23e+00 6.61e-01 2.39e+01 angle pdb=" C ASP A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta sigma weight residual 118.85 124.04 -5.19 1.09e+00 8.42e-01 2.27e+01 angle pdb=" N GLU A 371 " pdb=" CA GLU A 371 " pdb=" C GLU A 371 " ideal model delta sigma weight residual 112.90 106.91 5.99 1.31e+00 5.83e-01 2.09e+01 angle pdb=" O1A NAP A 500 " pdb=" PA NAP A 500 " pdb=" O2A NAP A 500 " ideal model delta sigma weight residual 121.77 109.73 12.04 3.00e+00 1.11e-01 1.61e+01 ... (remaining 4592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 1804 17.09 - 34.19: 157 34.19 - 51.28: 53 51.28 - 68.38: 20 68.38 - 85.47: 8 Dihedral angle restraints: 2042 sinusoidal: 848 harmonic: 1194 Sorted by residual: dihedral pdb=" CA ASP A 340 " pdb=" CB ASP A 340 " pdb=" CG ASP A 340 " pdb=" OD1 ASP A 340 " ideal model delta sinusoidal sigma weight residual -30.00 -86.22 56.22 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" N ARG A 246 " pdb=" CA ARG A 246 " pdb=" CB ARG A 246 " pdb=" CG ARG A 246 " ideal model delta sinusoidal sigma weight residual -180.00 -120.45 -59.55 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB LYS A 211 " pdb=" CG LYS A 211 " pdb=" CD LYS A 211 " pdb=" CE LYS A 211 " ideal model delta sinusoidal sigma weight residual 180.00 122.59 57.41 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 2039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 417 0.060 - 0.119: 69 0.119 - 0.179: 9 0.179 - 0.238: 1 0.238 - 0.298: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" C2B NAP A 500 " pdb=" C1B NAP A 500 " pdb=" C3B NAP A 500 " pdb=" O2B NAP A 500 " both_signs ideal model delta sigma weight residual False -2.75 -2.46 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA BARG A 370 " pdb=" N ARG A 370 " pdb=" C ARG A 370 " pdb=" CB BARG A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA GLU A 233 " pdb=" N GLU A 233 " pdb=" C GLU A 233 " pdb=" CB GLU A 233 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 494 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD AARG A 370 " 0.244 9.50e-02 1.11e+02 1.09e-01 7.34e+00 pdb=" NE AARG A 370 " -0.014 2.00e-02 2.50e+03 pdb=" CZ AARG A 370 " -0.003 2.00e-02 2.50e+03 pdb=" NH1AARG A 370 " -0.002 2.00e-02 2.50e+03 pdb=" NH2AARG A 370 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 58 " 0.198 9.50e-02 1.11e+02 8.86e-02 4.81e+00 pdb=" NE ARG A 58 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 58 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 58 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 58 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A 150 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.026 5.00e-02 4.00e+02 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 1377 2.93 - 3.42: 3361 3.42 - 3.92: 5832 3.92 - 4.41: 6746 4.41 - 4.90: 10881 Nonbonded interactions: 28197 Sorted by model distance: nonbonded pdb=" O PRO A 34 " pdb=" O HOH A 601 " model vdw 2.441 2.440 nonbonded pdb=" O ALA A 223 " pdb=" OG1 THR A 227 " model vdw 2.469 2.440 nonbonded pdb=" O LYS A 213 " pdb=" N THR A 238 " model vdw 2.489 2.520 nonbonded pdb=" N ASP A 145 " pdb=" OG1 THR A 148 " model vdw 2.504 2.520 nonbonded pdb=" OG1 THR A 68 " pdb=" OD1 ASP A 140 " model vdw 2.504 2.440 ... (remaining 28192 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=0.99 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: 0.710 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: 3.520 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 16.710 Find NCS groups from input model: 0.090 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 : 0.007 0.167 3382 Z= 0.469 Angle : 0.800 12.044 4597 Z= 0.435 Chirality : 0.048 0.298 497 Planarity : 0.007 0.109 585 Dihedral : 16.462 85.471 1282 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.95 % Allowed : 3.24 % Favored : 93.81 % 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: 1.22 (0.43), residues: 415 helix: 1.73 (0.36), residues: 212 sheet: -0.75 (0.66), residues: 70 loop : 0.37 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.001 0.000 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.6040 (OUTLIER) cc_final: 0.4799 (p0) outliers start: 10 outliers final: 2 residues processed: 72 average time/residue: 1.3968 time to fit residues: 103.0629 Evaluate side-chains 56 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 0.0570 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3382 Z= 0.227 Angle : 0.498 5.242 4597 Z= 0.258 Chirality : 0.043 0.121 497 Planarity : 0.005 0.046 585 Dihedral : 10.098 55.702 501 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.47 % Allowed : 10.03 % Favored : 88.50 % 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: 1.69 (0.43), residues: 415 helix: 2.10 (0.35), residues: 210 sheet: -0.15 (0.68), residues: 70 loop : 0.39 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 355 HIS 0.002 0.001 HIS A 61 PHE 0.009 0.001 PHE A 381 TYR 0.010 0.001 TYR A 363 ARG 0.002 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.6592 (p0) cc_final: 0.5716 (p0) outliers start: 5 outliers final: 1 residues processed: 59 average time/residue: 1.2634 time to fit residues: 76.6596 Evaluate side-chains 57 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3382 Z= 0.179 Angle : 0.459 4.916 4597 Z= 0.237 Chirality : 0.042 0.129 497 Planarity : 0.004 0.046 585 Dihedral : 7.426 50.123 493 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.47 % Allowed : 11.50 % Favored : 87.02 % 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: 1.90 (0.43), residues: 415 helix: 2.36 (0.34), residues: 210 sheet: 0.01 (0.68), residues: 70 loop : 0.28 (0.57), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.004 0.001 HIS A 267 PHE 0.010 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.6757 (p0) cc_final: 0.5827 (p0) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 1.3502 time to fit residues: 76.4111 Evaluate side-chains 55 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 149 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 0.0270 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3382 Z= 0.138 Angle : 0.441 4.741 4597 Z= 0.227 Chirality : 0.041 0.127 497 Planarity : 0.004 0.046 585 Dihedral : 6.872 53.523 493 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.59 % Allowed : 12.98 % Favored : 86.43 % 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: 2.08 (0.43), residues: 415 helix: 2.54 (0.35), residues: 210 sheet: 0.12 (0.69), residues: 70 loop : 0.30 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.007 0.001 HIS A 267 PHE 0.008 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.339 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 1.2757 time to fit residues: 72.1517 Evaluate side-chains 54 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 149 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3382 Z= 0.204 Angle : 0.460 4.820 4597 Z= 0.238 Chirality : 0.042 0.122 497 Planarity : 0.004 0.047 585 Dihedral : 6.695 54.828 493 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.59 % Allowed : 12.68 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.43), residues: 415 helix: 2.51 (0.35), residues: 209 sheet: 0.11 (0.69), residues: 70 loop : 0.12 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.008 0.001 HIS A 267 PHE 0.012 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.345 Fit side-chains REVERT: A 244 ASP cc_start: 0.6722 (p0) cc_final: 0.5515 (p0) outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 1.2804 time to fit residues: 69.8439 Evaluate side-chains 54 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3382 Z= 0.310 Angle : 0.505 5.195 4597 Z= 0.264 Chirality : 0.044 0.128 497 Planarity : 0.005 0.048 585 Dihedral : 6.733 53.981 493 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.59 % Allowed : 12.68 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.42), residues: 415 helix: 2.32 (0.34), residues: 209 sheet: 0.12 (0.69), residues: 70 loop : -0.03 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.008 0.002 HIS A 267 PHE 0.015 0.002 PHE A 381 TYR 0.013 0.002 TYR A 363 ARG 0.002 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.383 Fit side-chains REVERT: A 244 ASP cc_start: 0.6965 (p0) cc_final: 0.6647 (p0) outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 1.2870 time to fit residues: 72.8190 Evaluate side-chains 52 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3382 Z= 0.190 Angle : 0.469 5.141 4597 Z= 0.243 Chirality : 0.042 0.131 497 Planarity : 0.004 0.048 585 Dihedral : 6.488 54.795 493 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.88 % Allowed : 12.98 % Favored : 86.14 % 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: 1.90 (0.42), residues: 415 helix: 2.46 (0.34), residues: 208 sheet: 0.19 (0.69), residues: 70 loop : 0.02 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.009 0.002 HIS A 267 PHE 0.011 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.374 Fit side-chains REVERT: A 244 ASP cc_start: 0.6812 (p0) cc_final: 0.6496 (p0) REVERT: A 290 ASP cc_start: 0.8058 (m-30) cc_final: 0.7847 (t70) outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 1.3343 time to fit residues: 72.7867 Evaluate side-chains 55 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3382 Z= 0.131 Angle : 0.438 4.789 4597 Z= 0.225 Chirality : 0.041 0.129 497 Planarity : 0.004 0.048 585 Dihedral : 6.195 56.662 493 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.88 % Allowed : 13.27 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.42), residues: 415 helix: 2.60 (0.35), residues: 208 sheet: 0.18 (0.69), residues: 70 loop : 0.09 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.009 0.001 HIS A 267 PHE 0.009 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.383 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 58 average time/residue: 1.2359 time to fit residues: 73.9078 Evaluate side-chains 56 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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: 0.8610 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3382 Z= 0.142 Angle : 0.455 4.572 4597 Z= 0.234 Chirality : 0.041 0.125 497 Planarity : 0.004 0.047 585 Dihedral : 6.219 58.116 493 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.59 % Allowed : 14.75 % Favored : 84.66 % 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: 2.02 (0.42), residues: 415 helix: 2.60 (0.35), residues: 208 sheet: 0.10 (0.67), residues: 70 loop : 0.10 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.005 0.001 HIS A 267 PHE 0.010 0.001 PHE A 381 TYR 0.009 0.001 TYR A 226 ARG 0.001 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.6789 (p0) cc_final: 0.6370 (p0) outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 1.2598 time to fit residues: 70.0444 Evaluate side-chains 56 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.8634 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3382 Z= 0.188 Angle : 0.467 4.708 4597 Z= 0.242 Chirality : 0.042 0.126 497 Planarity : 0.004 0.047 585 Dihedral : 6.256 58.196 493 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.59 % Allowed : 14.75 % Favored : 84.66 % 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: 2.06 (0.42), residues: 415 helix: 2.66 (0.35), residues: 202 sheet: 0.06 (0.64), residues: 75 loop : 0.23 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.008 0.001 HIS A 267 PHE 0.012 0.001 PHE A 381 TYR 0.010 0.001 TYR A 226 ARG 0.001 0.000 ARG A 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.361 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 55 average time/residue: 1.1988 time to fit residues: 67.9710 Evaluate side-chains 55 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 0.0370 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.088314 restraints weight = 11779.645| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.64 r_work: 0.2738 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3382 Z= 0.138 Angle : 0.448 4.590 4597 Z= 0.231 Chirality : 0.041 0.127 497 Planarity : 0.004 0.047 585 Dihedral : 6.155 58.277 493 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.29 % Allowed : 15.04 % Favored : 84.66 % 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: 2.11 (0.42), residues: 415 helix: 2.73 (0.35), residues: 202 sheet: 0.07 (0.64), residues: 75 loop : 0.23 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.007 0.001 HIS A 267 PHE 0.010 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1895.24 seconds wall clock time: 34 minutes 9.49 seconds (2049.49 seconds total)