Starting phenix.real_space_refine on Fri Apr 5 12:39:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/04_2024/8pij_17683_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/04_2024/8pij_17683.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/04_2024/8pij_17683_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/04_2024/8pij_17683_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/04_2024/8pij_17683_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/04_2024/8pij_17683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/04_2024/8pij_17683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/04_2024/8pij_17683_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/04_2024/8pij_17683_updated.pdb" } resolution = 2.9 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= 0.022 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 1 5.49 5 S 10 5.16 5 C 1362 2.51 5 N 376 2.21 5 O 442 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-5288/modules/chem_data/mon_lib" Total number of atoms: 2191 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1197 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 965 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'G3P': 1, 'WKE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.65, per 1000 atoms: 0.75 Number of scatterers: 2191 At special positions: 0 Unit cell: (71.61, 65.1, 117.18, 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 10 16.00 P 1 15.00 O 442 8.00 N 376 7.00 C 1362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 111 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 457.3 milliseconds 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 7 helices and 3 sheets defined 21.5% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 Processing helix chain 'A' and resid 24 through 54 removed outlier: 4.215A pdb=" N GLU A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing sheet with id= A, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.540A pdb=" N GLY A 121 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 79 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.556A pdb=" N GLN B 5 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 123 through 125 removed outlier: 3.528A pdb=" N ALA B 125 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 36 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 51 " --> pdb=" O TRP B 38 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ARG B 40 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) 75 hydrogen bonds defined for protein. 210 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: 0.57 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 619 1.33 - 1.45: 377 1.45 - 1.57: 1215 1.57 - 1.69: 1 1.69 - 1.81: 14 Bond restraints: 2226 Sorted by residual: bond pdb=" N WKE A 202 " pdb=" C4 WKE A 202 " ideal model delta sigma weight residual 1.481 1.329 0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" C8 WKE A 202 " pdb=" N1 WKE A 202 " ideal model delta sigma weight residual 1.456 1.330 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " ideal model delta sigma weight residual 1.726 1.608 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" O WKE A 202 " pdb=" C2 WKE A 202 " ideal model delta sigma weight residual 1.522 1.427 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C8 WKE A 202 " pdb=" C9 WKE A 202 " ideal model delta sigma weight residual 1.586 1.499 0.087 2.00e-02 2.50e+03 1.90e+01 ... (remaining 2221 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.67: 40 106.67 - 113.50: 1248 113.50 - 120.33: 736 120.33 - 127.16: 976 127.16 - 133.99: 19 Bond angle restraints: 3019 Sorted by residual: angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 100.65 109.90 -9.25 3.00e+00 1.11e-01 9.51e+00 angle pdb=" N ASP B 109 " pdb=" CA ASP B 109 " pdb=" CB ASP B 109 " ideal model delta sigma weight residual 111.65 107.89 3.76 1.40e+00 5.10e-01 7.20e+00 angle pdb=" CA TYR B 113 " pdb=" CB TYR B 113 " pdb=" CG TYR B 113 " ideal model delta sigma weight residual 113.90 118.11 -4.21 1.80e+00 3.09e-01 5.46e+00 angle pdb=" C PHE B 29 " pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " ideal model delta sigma weight residual 110.42 114.66 -4.24 1.99e+00 2.53e-01 4.55e+00 angle pdb=" N SER B 114 " pdb=" CA SER B 114 " pdb=" C SER B 114 " ideal model delta sigma weight residual 109.50 112.74 -3.24 1.58e+00 4.01e-01 4.20e+00 ... (remaining 3014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.53: 1072 13.53 - 27.07: 158 27.07 - 40.60: 64 40.60 - 54.14: 27 54.14 - 67.67: 15 Dihedral angle restraints: 1336 sinusoidal: 507 harmonic: 829 Sorted by residual: dihedral pdb=" N ARG B 47 " pdb=" CA ARG B 47 " pdb=" CB ARG B 47 " pdb=" CG ARG B 47 " ideal model delta sinusoidal sigma weight residual -60.00 -119.62 59.62 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG B 103 " pdb=" CB ARG B 103 " pdb=" CG ARG B 103 " pdb=" CD ARG B 103 " ideal model delta sinusoidal sigma weight residual -180.00 -122.02 -57.98 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CB ARG B 21 " pdb=" CG ARG B 21 " pdb=" CD ARG B 21 " pdb=" NE ARG B 21 " ideal model delta sinusoidal sigma weight residual -60.00 -117.94 57.94 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 1333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 183 0.023 - 0.046: 78 0.046 - 0.069: 53 0.069 - 0.093: 17 0.093 - 0.116: 18 Chirality restraints: 349 Sorted by residual: chirality pdb=" CA VAL B 81 " pdb=" N VAL B 81 " pdb=" C VAL B 81 " pdb=" CB VAL B 81 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA VAL A 80 " pdb=" N VAL A 80 " pdb=" C VAL A 80 " pdb=" CB VAL A 80 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.15e-01 ... (remaining 346 not shown) Planarity restraints: 383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 WKE A 202 " 0.036 2.00e-02 2.50e+03 2.93e-02 1.08e+01 pdb=" C8 WKE A 202 " -0.010 2.00e-02 2.50e+03 pdb=" C9 WKE A 202 " 0.027 2.00e-02 2.50e+03 pdb=" N1 WKE A 202 " -0.046 2.00e-02 2.50e+03 pdb=" O3 WKE A 202 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 108 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C SER B 108 " 0.052 2.00e-02 2.50e+03 pdb=" O SER B 108 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP B 109 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WKE A 202 " -0.018 2.00e-02 2.50e+03 1.15e-02 1.66e+00 pdb=" C3 WKE A 202 " 0.014 2.00e-02 2.50e+03 pdb=" C4 WKE A 202 " -0.004 2.00e-02 2.50e+03 pdb=" C5 WKE A 202 " 0.011 2.00e-02 2.50e+03 pdb=" O1 WKE A 202 " -0.003 2.00e-02 2.50e+03 ... (remaining 380 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 365 2.76 - 3.30: 1781 3.30 - 3.83: 3381 3.83 - 4.37: 3817 4.37 - 4.90: 6916 Nonbonded interactions: 16260 Sorted by model distance: nonbonded pdb=" O ALA A 31 " pdb=" OG SER A 34 " model vdw 2.231 2.440 nonbonded pdb=" OD2 ASP A 60 " pdb=" OG SER B 108 " model vdw 2.260 2.440 nonbonded pdb=" NH2 ARG B 103 " pdb=" O1 WKE A 202 " model vdw 2.348 2.520 nonbonded pdb=" OG1 THR A 81 " pdb=" O3P G3P A 201 " model vdw 2.355 2.440 nonbonded pdb=" OG SER B 56 " pdb=" O SER B 108 " model vdw 2.356 2.440 ... (remaining 16255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 12.450 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.400 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 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 0.152 2226 Z= 0.559 Angle : 0.577 9.250 3019 Z= 0.290 Chirality : 0.041 0.116 349 Planarity : 0.004 0.031 383 Dihedral : 17.939 67.669 797 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.46 % Allowed : 30.74 % Favored : 65.80 % 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: 0.25 (0.52), residues: 284 helix: 1.24 (0.72), residues: 50 sheet: 0.22 (0.59), residues: 83 loop : -0.14 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 108 HIS 0.000 0.000 HIS A 149 PHE 0.002 0.001 PHE A 119 TYR 0.018 0.001 TYR B 113 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8356 (tt0) cc_final: 0.8044 (tt0) REVERT: B 75 ASP cc_start: 0.8350 (t0) cc_final: 0.7405 (t0) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.9192 time to fit residues: 58.4614 Evaluate side-chains 52 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 0.0030 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- 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: 0.8798 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2226 Z= 0.176 Angle : 0.480 4.607 3019 Z= 0.257 Chirality : 0.042 0.149 349 Planarity : 0.003 0.026 383 Dihedral : 7.226 52.794 333 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.06 % Allowed : 33.77 % Favored : 60.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.52), residues: 284 helix: 1.09 (0.72), residues: 52 sheet: 0.30 (0.54), residues: 92 loop : -0.26 (0.58), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.006 0.001 PHE B 102 TYR 0.008 0.001 TYR B 118 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 0.239 Fit side-chains REVERT: A 41 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: B 47 ARG cc_start: 0.8709 (ttp-170) cc_final: 0.8491 (ttp-170) REVERT: B 75 ASP cc_start: 0.8109 (t0) cc_final: 0.7609 (t70) outliers start: 14 outliers final: 6 residues processed: 51 average time/residue: 1.0237 time to fit residues: 53.5120 Evaluate side-chains 49 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2226 Z= 0.201 Angle : 0.503 7.157 3019 Z= 0.262 Chirality : 0.042 0.141 349 Planarity : 0.003 0.033 383 Dihedral : 5.886 51.313 330 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.19 % Allowed : 32.90 % Favored : 61.90 % 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: 0.02 (0.50), residues: 284 helix: 1.14 (0.70), residues: 52 sheet: -0.01 (0.53), residues: 84 loop : -0.29 (0.56), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.008 0.001 TYR B 118 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.257 Fit side-chains REVERT: A 41 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8054 (tt0) outliers start: 12 outliers final: 5 residues processed: 48 average time/residue: 0.9461 time to fit residues: 46.6622 Evaluate side-chains 47 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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: 0.8825 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2226 Z= 0.180 Angle : 0.480 4.528 3019 Z= 0.256 Chirality : 0.042 0.139 349 Planarity : 0.003 0.028 383 Dihedral : 5.746 56.828 329 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.06 % Allowed : 32.03 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.50), residues: 284 helix: 1.20 (0.69), residues: 52 sheet: 0.39 (0.53), residues: 77 loop : -0.35 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE B 102 TYR 0.007 0.001 TYR B 96 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.231 Fit side-chains REVERT: A 41 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7996 (tt0) outliers start: 14 outliers final: 6 residues processed: 48 average time/residue: 1.1072 time to fit residues: 54.3737 Evaluate side-chains 45 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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: 0.8838 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2226 Z= 0.215 Angle : 0.518 7.116 3019 Z= 0.269 Chirality : 0.043 0.140 349 Planarity : 0.003 0.030 383 Dihedral : 5.725 55.275 329 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.19 % Allowed : 30.30 % Favored : 64.50 % 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: 0.29 (0.50), residues: 284 helix: 1.41 (0.70), residues: 52 sheet: 0.51 (0.53), residues: 77 loop : -0.36 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.007 0.001 TYR B 96 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.285 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 47 average time/residue: 1.0581 time to fit residues: 50.9289 Evaluate side-chains 42 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.8855 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2226 Z= 0.267 Angle : 0.542 6.101 3019 Z= 0.286 Chirality : 0.043 0.140 349 Planarity : 0.003 0.033 383 Dihedral : 5.637 49.375 329 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.46 % Allowed : 31.17 % Favored : 65.37 % 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: 0.30 (0.50), residues: 284 helix: 1.52 (0.70), residues: 52 sheet: 0.60 (0.53), residues: 76 loop : -0.43 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE A 119 TYR 0.007 0.001 TYR B 82 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.253 Fit side-chains REVERT: B 93 THR cc_start: 0.8806 (p) cc_final: 0.8581 (p) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 1.0677 time to fit residues: 47.0528 Evaluate side-chains 43 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.8833 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2226 Z= 0.184 Angle : 0.538 7.724 3019 Z= 0.274 Chirality : 0.042 0.141 349 Planarity : 0.003 0.035 383 Dihedral : 5.449 49.296 329 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.33 % Allowed : 32.03 % Favored : 63.64 % 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: 0.53 (0.50), residues: 284 helix: 1.89 (0.72), residues: 51 sheet: 0.74 (0.55), residues: 76 loop : -0.34 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.007 0.001 TYR B 96 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.240 Fit side-chains REVERT: B 93 THR cc_start: 0.8789 (p) cc_final: 0.8578 (p) outliers start: 10 outliers final: 7 residues processed: 44 average time/residue: 1.0705 time to fit residues: 48.2723 Evaluate side-chains 43 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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: 0.8849 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2226 Z= 0.230 Angle : 0.541 5.401 3019 Z= 0.283 Chirality : 0.043 0.134 349 Planarity : 0.003 0.036 383 Dihedral : 5.441 49.186 329 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.46 % Allowed : 31.60 % Favored : 64.94 % 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: 0.49 (0.50), residues: 284 helix: 1.86 (0.72), residues: 51 sheet: 0.71 (0.55), residues: 76 loop : -0.37 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.006 0.001 TYR B 118 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.208 Fit side-chains REVERT: B 93 THR cc_start: 0.8764 (p) cc_final: 0.8532 (p) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 1.0143 time to fit residues: 44.6634 Evaluate side-chains 41 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 32 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 0.1980 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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: 0.8801 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2226 Z= 0.144 Angle : 0.543 8.626 3019 Z= 0.273 Chirality : 0.042 0.136 349 Planarity : 0.003 0.036 383 Dihedral : 4.446 41.483 328 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.60 % Allowed : 33.33 % Favored : 64.07 % 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: 0.73 (0.51), residues: 284 helix: 2.09 (0.74), residues: 51 sheet: 0.75 (0.56), residues: 77 loop : -0.16 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.006 0.001 TYR B 118 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.254 Fit side-chains REVERT: A 41 GLU cc_start: 0.9009 (tm-30) cc_final: 0.7921 (tt0) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 1.1417 time to fit residues: 47.9766 Evaluate side-chains 39 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8807 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2226 Z= 0.153 Angle : 0.525 5.382 3019 Z= 0.277 Chirality : 0.042 0.145 349 Planarity : 0.003 0.037 383 Dihedral : 4.390 41.686 328 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.73 % Allowed : 32.47 % Favored : 65.80 % 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: 0.75 (0.52), residues: 284 helix: 2.12 (0.74), residues: 51 sheet: 0.69 (0.57), residues: 77 loop : -0.10 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.007 0.001 TYR B 82 ARG 0.001 0.000 ARG A 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.196 Fit side-chains REVERT: B 41 GLN cc_start: 0.8642 (tp40) cc_final: 0.8400 (tp-100) outliers start: 4 outliers final: 4 residues processed: 39 average time/residue: 1.1788 time to fit residues: 47.0156 Evaluate side-chains 39 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.0170 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.3111 r_free = 0.3111 target = 0.062957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.042498 restraints weight = 6410.090| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 3.18 r_work: 0.2469 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2359 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2226 Z= 0.145 Angle : 0.553 8.529 3019 Z= 0.285 Chirality : 0.043 0.189 349 Planarity : 0.003 0.038 383 Dihedral : 4.253 41.816 328 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.73 % Allowed : 33.77 % Favored : 64.50 % 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: 0.89 (0.53), residues: 284 helix: 2.15 (0.75), residues: 51 sheet: 0.79 (0.56), residues: 82 loop : -0.00 (0.56), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.006 0.001 TYR B 96 ARG 0.000 0.000 ARG A 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1524.29 seconds wall clock time: 27 minutes 41.48 seconds (1661.48 seconds total)