Starting phenix.real_space_refine on Sun Mar 10 19:32:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byl_16327/03_2024/8byl_16327_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byl_16327/03_2024/8byl_16327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byl_16327/03_2024/8byl_16327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byl_16327/03_2024/8byl_16327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byl_16327/03_2024/8byl_16327_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byl_16327/03_2024/8byl_16327_updated.pdb" } resolution = 3.5 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= 0.028 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 24 5.16 5 C 2775 2.51 5 N 745 2.21 5 O 833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1017": "OD1" <-> "OD2" Residue "A ASP 1043": "OD1" <-> "OD2" Residue "A ASP 1089": "OD1" <-> "OD2" Residue "A TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1117": "OD1" <-> "OD2" Residue "A GLU 1133": "OE1" <-> "OE2" Residue "A GLU 1134": "OE1" <-> "OE2" Residue "A ASP 1144": "OD1" <-> "OD2" Residue "A GLU 1148": "OE1" <-> "OE2" Residue "B GLU 2103": "OE1" <-> "OE2" Residue "B ASP 2133": "OD1" <-> "OD2" Residue "C GLU 3015": "OE1" <-> "OE2" Residue "C PHE 3017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4185": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4378 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1111 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ASP:plan': 4, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2585 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 317} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 584 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 63} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 98 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TPO:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.83, per 1000 atoms: 0.65 Number of scatterers: 4378 At special positions: 0 Unit cell: (80.25, 113.42, 74.9, 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 24 16.00 P 1 15.00 O 833 8.00 N 745 7.00 C 2775 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: 1.81 Conformation dependent library (CDL) restraints added in 832.8 milliseconds 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 3 sheets defined 34.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 1025 through 1032 removed outlier: 3.899A pdb=" N GLU A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1056 Processing helix chain 'A' and resid 1069 through 1073 Processing helix chain 'A' and resid 1075 through 1080 Processing helix chain 'A' and resid 1090 through 1093 No H-bonds generated for 'chain 'A' and resid 1090 through 1093' Processing helix chain 'A' and resid 1097 through 1110 Processing helix chain 'A' and resid 1113 through 1126 removed outlier: 3.903A pdb=" N CYS A1120 " --> pdb=" O LEU A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1139 removed outlier: 3.992A pdb=" N ARG A1136 " --> pdb=" O PRO A1132 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1156 removed outlier: 3.624A pdb=" N VAL A1153 " --> pdb=" O GLU A1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2102 through 2111 removed outlier: 3.500A pdb=" N GLY B2107 " --> pdb=" O GLU B2103 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS B2111 " --> pdb=" O GLY B2107 " (cutoff:3.500A) Processing helix chain 'B' and resid 2114 through 2117 No H-bonds generated for 'chain 'B' and resid 2114 through 2117' Processing helix chain 'B' and resid 2119 through 2122 Processing helix chain 'B' and resid 2125 through 2131 Processing helix chain 'B' and resid 2149 through 2157 Processing helix chain 'B' and resid 2195 through 2202 Processing helix chain 'B' and resid 2220 through 2228 removed outlier: 3.742A pdb=" N ALA B2227 " --> pdb=" O VAL B2223 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS B2228 " --> pdb=" O ASN B2224 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2254 Processing helix chain 'B' and resid 2271 through 2280 Processing helix chain 'B' and resid 2294 through 2296 No H-bonds generated for 'chain 'B' and resid 2294 through 2296' Processing helix chain 'B' and resid 2299 through 2308 Processing helix chain 'B' and resid 2325 through 2333 removed outlier: 3.962A pdb=" N PHE B2328 " --> pdb=" O ASN B2325 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B2329 " --> pdb=" O ASP B2326 " (cutoff:3.500A) Processing helix chain 'B' and resid 2351 through 2358 Processing helix chain 'B' and resid 2375 through 2381 Processing helix chain 'C' and resid 3026 through 3031 removed outlier: 4.156A pdb=" N LYS C3030 " --> pdb=" O LYS C3026 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU C3031 " --> pdb=" O ASP C3027 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3026 through 3031' Processing helix chain 'C' and resid 3040 through 3043 No H-bonds generated for 'chain 'C' and resid 3040 through 3043' Processing sheet with id= A, first strand: chain 'B' and resid 2162 through 2164 removed outlier: 7.229A pdb=" N HIS B2185 " --> pdb=" O PHE B2163 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 2210 through 2212 removed outlier: 6.455A pdb=" N ARG B2234 " --> pdb=" O LEU B2211 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU B2260 " --> pdb=" O LEU B2235 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 3012 through 3014 97 hydrogen bonds defined for protein. 255 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: 0.90 Time building geometry restraints manager: 1.95 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: 921 1.33 - 1.45: 962 1.45 - 1.57: 2555 1.57 - 1.69: 1 1.69 - 1.81: 31 Bond restraints: 4470 Sorted by residual: bond pdb=" OG1 TPO D4187 " pdb=" P TPO D4187 " ideal model delta sigma weight residual 1.717 1.604 0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" CB TPO D4187 " pdb=" OG1 TPO D4187 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" C PRO A1070 " pdb=" N PRO A1071 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.18e-02 7.18e+03 8.23e+00 bond pdb=" N LEU B2130 " pdb=" CA LEU B2130 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.31e-02 5.83e+03 6.03e+00 bond pdb=" C PRO A1132 " pdb=" O PRO A1132 " ideal model delta sigma weight residual 1.238 1.209 0.029 1.37e-02 5.33e+03 4.47e+00 ... (remaining 4465 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.06: 161 107.06 - 113.82: 2533 113.82 - 120.57: 1732 120.57 - 127.32: 1607 127.32 - 134.07: 59 Bond angle restraints: 6092 Sorted by residual: angle pdb=" N PRO A1072 " pdb=" CA PRO A1072 " pdb=" CB PRO A1072 " ideal model delta sigma weight residual 103.33 109.89 -6.56 1.10e+00 8.26e-01 3.56e+01 angle pdb=" C PRO A1132 " pdb=" CA PRO A1132 " pdb=" CB PRO A1132 " ideal model delta sigma weight residual 111.44 103.18 8.26 1.51e+00 4.39e-01 3.00e+01 angle pdb=" C TYR C3012 " pdb=" N ASP C3013 " pdb=" CA ASP C3013 " ideal model delta sigma weight residual 122.82 114.23 8.59 1.68e+00 3.54e-01 2.62e+01 angle pdb=" C ARG B2294 " pdb=" CA ARG B2294 " pdb=" CB ARG B2294 " ideal model delta sigma weight residual 116.63 111.53 5.10 1.16e+00 7.43e-01 1.94e+01 angle pdb=" N ASP A1084 " pdb=" CA ASP A1084 " pdb=" C ASP A1084 " ideal model delta sigma weight residual 108.31 101.83 6.48 1.52e+00 4.33e-01 1.82e+01 ... (remaining 6087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 2323 17.64 - 35.29: 291 35.29 - 52.93: 58 52.93 - 70.58: 15 70.58 - 88.22: 7 Dihedral angle restraints: 2694 sinusoidal: 1026 harmonic: 1668 Sorted by residual: dihedral pdb=" CA VAL A1087 " pdb=" C VAL A1087 " pdb=" N TRP A1088 " pdb=" CA TRP A1088 " ideal model delta harmonic sigma weight residual -180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA PRO B2384 " pdb=" C PRO B2384 " pdb=" N HIS B2385 " pdb=" CA HIS B2385 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" C PRO A1132 " pdb=" N PRO A1132 " pdb=" CA PRO A1132 " pdb=" CB PRO A1132 " ideal model delta harmonic sigma weight residual -120.70 -111.79 -8.91 0 2.50e+00 1.60e-01 1.27e+01 ... (remaining 2691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 526 0.046 - 0.092: 138 0.092 - 0.138: 40 0.138 - 0.184: 4 0.184 - 0.230: 4 Chirality restraints: 712 Sorted by residual: chirality pdb=" CA PRO A1072 " pdb=" N PRO A1072 " pdb=" C PRO A1072 " pdb=" CB PRO A1072 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA LEU B2416 " pdb=" N LEU B2416 " pdb=" C LEU B2416 " pdb=" CB LEU B2416 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE A1112 " pdb=" CA ILE A1112 " pdb=" CG1 ILE A1112 " pdb=" CG2 ILE A1112 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 709 not shown) Planarity restraints: 785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B2169 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C PHE B2169 " 0.037 2.00e-02 2.50e+03 pdb=" O PHE B2169 " -0.014 2.00e-02 2.50e+03 pdb=" N MET B2170 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1085 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A1086 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A1086 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1086 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1045 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A1046 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A1046 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1046 " 0.025 5.00e-02 4.00e+02 ... (remaining 782 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1347 2.82 - 3.34: 4101 3.34 - 3.86: 6824 3.86 - 4.38: 7789 4.38 - 4.90: 13394 Nonbonded interactions: 33455 Sorted by model distance: nonbonded pdb=" N GLU A1019 " pdb=" OE1 GLU A1019 " model vdw 2.304 2.520 nonbonded pdb=" OD1 ASP B2316 " pdb=" OG SER B2318 " model vdw 2.309 2.440 nonbonded pdb=" O LEU B2118 " pdb=" OG SER B2121 " model vdw 2.318 2.440 nonbonded pdb=" O THR B2139 " pdb=" OG1 THR B2139 " model vdw 2.354 2.440 nonbonded pdb=" NE1 TRP B2265 " pdb=" OG SER C3041 " model vdw 2.355 2.520 ... (remaining 33450 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 group one per residue 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.760 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.510 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.004 0.113 4470 Z= 0.246 Angle : 0.657 8.592 6092 Z= 0.385 Chirality : 0.047 0.230 712 Planarity : 0.004 0.049 785 Dihedral : 16.827 88.221 1602 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.05 % Allowed : 23.16 % Favored : 75.79 % 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: -1.39 (0.36), residues: 558 helix: -0.13 (0.40), residues: 185 sheet: -1.76 (0.77), residues: 48 loop : -1.26 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1088 HIS 0.003 0.001 HIS B2339 PHE 0.010 0.001 PHE B2267 TYR 0.008 0.001 TYR A1109 ARG 0.002 0.000 ARG B2294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: B 2332 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7916 (m-80) outliers start: 5 outliers final: 1 residues processed: 77 average time/residue: 0.1708 time to fit residues: 16.7775 Evaluate side-chains 77 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2147 LEU Chi-restraints excluded: chain B residue 2332 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.3980 chunk 41 optimal weight: 0.1980 chunk 23 optimal weight: 0.0770 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4470 Z= 0.163 Angle : 0.531 6.472 6092 Z= 0.272 Chirality : 0.043 0.149 712 Planarity : 0.004 0.053 785 Dihedral : 4.820 44.743 601 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.74 % Allowed : 23.16 % Favored : 74.11 % 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: -1.33 (0.36), residues: 558 helix: -0.17 (0.39), residues: 186 sheet: -1.79 (0.76), residues: 48 loop : -1.14 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.006 0.001 PHE B2267 TYR 0.011 0.001 TYR C3012 ARG 0.001 0.000 ARG B2129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.7568 (t80) cc_final: 0.7362 (t80) REVERT: C 3012 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.5883 (p90) REVERT: C 3021 HIS cc_start: 0.8320 (p90) cc_final: 0.8111 (p90) outliers start: 13 outliers final: 9 residues processed: 83 average time/residue: 0.1589 time to fit residues: 17.0071 Evaluate side-chains 84 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4470 Z= 0.296 Angle : 0.617 7.735 6092 Z= 0.315 Chirality : 0.045 0.157 712 Planarity : 0.004 0.053 785 Dihedral : 4.583 19.216 597 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.00 % Allowed : 23.58 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.36), residues: 558 helix: -0.22 (0.39), residues: 186 sheet: -2.11 (0.74), residues: 50 loop : -1.22 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.012 0.002 PHE C3069 TYR 0.013 0.002 TYR C3012 ARG 0.003 0.000 ARG C3020 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.7750 (t80) cc_final: 0.7420 (t80) REVERT: C 3012 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.5772 (p90) outliers start: 19 outliers final: 11 residues processed: 88 average time/residue: 0.1686 time to fit residues: 18.8343 Evaluate side-chains 85 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2223 VAL Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3066 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4470 Z= 0.196 Angle : 0.553 6.951 6092 Z= 0.284 Chirality : 0.043 0.139 712 Planarity : 0.004 0.052 785 Dihedral : 4.389 17.556 597 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.42 % Allowed : 23.79 % Favored : 71.79 % 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: -1.36 (0.36), residues: 558 helix: -0.11 (0.40), residues: 185 sheet: -1.14 (0.97), residues: 31 loop : -1.37 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.012 0.001 PHE B2169 TYR 0.012 0.001 TYR A1109 ARG 0.003 0.000 ARG B2257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.7803 (t80) cc_final: 0.7466 (t80) REVERT: B 2169 PHE cc_start: 0.8472 (t80) cc_final: 0.8246 (t80) REVERT: C 3012 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.6096 (p90) outliers start: 21 outliers final: 15 residues processed: 90 average time/residue: 0.1644 time to fit residues: 18.8009 Evaluate side-chains 90 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2147 LEU Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2197 THR Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2345 CYS Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.0570 chunk 21 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 0.0770 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2224 ASN C3021 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4470 Z= 0.151 Angle : 0.526 6.345 6092 Z= 0.272 Chirality : 0.043 0.142 712 Planarity : 0.004 0.051 785 Dihedral : 4.077 17.459 597 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.79 % Allowed : 24.63 % Favored : 71.58 % 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: -1.21 (0.37), residues: 558 helix: 0.00 (0.40), residues: 185 sheet: -1.59 (0.92), residues: 38 loop : -1.18 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.007 0.001 PHE B2169 TYR 0.018 0.001 TYR A1109 ARG 0.002 0.000 ARG B2257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.7794 (t80) cc_final: 0.7500 (t80) REVERT: C 3012 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6218 (p90) REVERT: C 3021 HIS cc_start: 0.8244 (p-80) cc_final: 0.7883 (p-80) outliers start: 18 outliers final: 12 residues processed: 86 average time/residue: 0.1676 time to fit residues: 18.3297 Evaluate side-chains 86 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2116 GLU Chi-restraints excluded: chain B residue 2147 LEU Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3048 VAL Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7577 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4470 Z= 0.206 Angle : 0.560 6.537 6092 Z= 0.288 Chirality : 0.043 0.147 712 Planarity : 0.004 0.049 785 Dihedral : 4.215 17.257 597 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.05 % Allowed : 23.37 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.37), residues: 558 helix: 0.00 (0.40), residues: 186 sheet: -2.41 (0.65), residues: 64 loop : -0.91 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C3043 HIS 0.003 0.001 HIS C3021 PHE 0.007 0.001 PHE B2267 TYR 0.021 0.002 TYR A1109 ARG 0.004 0.000 ARG B2257 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: C 3012 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.6071 (p90) outliers start: 24 outliers final: 17 residues processed: 92 average time/residue: 0.1355 time to fit residues: 16.6528 Evaluate side-chains 90 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2147 LEU Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2197 THR Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2345 CYS Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3048 VAL Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Chi-restraints excluded: chain C residue 3066 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4470 Z= 0.204 Angle : 0.570 7.190 6092 Z= 0.290 Chirality : 0.044 0.176 712 Planarity : 0.004 0.048 785 Dihedral : 4.207 17.208 597 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.84 % Allowed : 24.21 % Favored : 70.95 % 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: -1.19 (0.37), residues: 558 helix: 0.05 (0.40), residues: 186 sheet: -2.34 (0.66), residues: 64 loop : -0.90 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C3043 HIS 0.004 0.001 HIS B2339 PHE 0.009 0.001 PHE A1014 TYR 0.021 0.001 TYR A1109 ARG 0.004 0.000 ARG B2257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: C 3012 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.6109 (p90) outliers start: 23 outliers final: 18 residues processed: 85 average time/residue: 0.1391 time to fit residues: 15.6199 Evaluate side-chains 88 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 69 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2147 LEU Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2197 THR Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2345 CYS Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Chi-restraints excluded: chain C residue 3066 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.0040 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 0.0170 chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.4430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4470 Z= 0.176 Angle : 0.553 6.807 6092 Z= 0.283 Chirality : 0.043 0.145 712 Planarity : 0.004 0.048 785 Dihedral : 4.104 17.225 597 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.42 % Allowed : 24.63 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.37), residues: 558 helix: 0.10 (0.40), residues: 185 sheet: -1.76 (0.84), residues: 43 loop : -1.16 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.009 0.001 PHE A1014 TYR 0.020 0.002 TYR A1109 ARG 0.003 0.000 ARG B2257 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 73 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: B 2129 ARG cc_start: 0.7965 (tmm-80) cc_final: 0.7225 (mtm180) REVERT: B 2169 PHE cc_start: 0.8367 (t80) cc_final: 0.8049 (t80) REVERT: C 3012 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.6262 (p90) outliers start: 21 outliers final: 18 residues processed: 86 average time/residue: 0.1418 time to fit residues: 16.1681 Evaluate side-chains 91 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2147 LEU Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2197 THR Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2345 CYS Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3048 VAL Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Chi-restraints excluded: chain C residue 3066 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4470 Z= 0.210 Angle : 0.575 7.297 6092 Z= 0.294 Chirality : 0.044 0.146 712 Planarity : 0.004 0.047 785 Dihedral : 4.179 17.055 597 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.84 % Allowed : 24.42 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.37), residues: 558 helix: 0.08 (0.40), residues: 186 sheet: -2.31 (0.66), residues: 64 loop : -0.92 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.011 0.001 PHE A1014 TYR 0.022 0.002 TYR A1109 ARG 0.003 0.000 ARG B2257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 74 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: B 2129 ARG cc_start: 0.7917 (tmm-80) cc_final: 0.7171 (mtm180) REVERT: C 3012 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.6122 (p90) outliers start: 23 outliers final: 20 residues processed: 88 average time/residue: 0.1370 time to fit residues: 16.0786 Evaluate side-chains 94 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 73 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2147 LEU Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2197 THR Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2297 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2345 CYS Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3048 VAL Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Chi-restraints excluded: chain C residue 3066 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 50 optimal weight: 0.3980 chunk 43 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4470 Z= 0.197 Angle : 0.570 7.451 6092 Z= 0.292 Chirality : 0.044 0.144 712 Planarity : 0.004 0.048 785 Dihedral : 4.216 17.357 597 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.63 % Allowed : 24.63 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.36), residues: 558 helix: 0.11 (0.40), residues: 185 sheet: -1.80 (0.83), residues: 43 loop : -1.18 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.012 0.001 PHE A1014 TYR 0.021 0.002 TYR A1109 ARG 0.003 0.000 ARG B2257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 73 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: B 2129 ARG cc_start: 0.7886 (tmm-80) cc_final: 0.7137 (mtm180) REVERT: C 3012 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.6157 (p90) REVERT: C 3021 HIS cc_start: 0.8379 (p90) cc_final: 0.8176 (p90) outliers start: 22 outliers final: 19 residues processed: 86 average time/residue: 0.1381 time to fit residues: 15.7461 Evaluate side-chains 92 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2147 LEU Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2197 THR Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2297 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2345 CYS Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3048 VAL Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Chi-restraints excluded: chain C residue 3066 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 chunk 2 optimal weight: 0.0000 chunk 31 optimal weight: 2.9990 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.205362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.156594 restraints weight = 5055.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.161439 restraints weight = 3074.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164886 restraints weight = 2208.909| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4470 Z= 0.164 Angle : 0.553 7.276 6092 Z= 0.284 Chirality : 0.043 0.142 712 Planarity : 0.004 0.049 785 Dihedral : 4.036 17.352 597 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.00 % Allowed : 25.47 % Favored : 70.53 % 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: -1.08 (0.36), residues: 558 helix: 0.16 (0.40), residues: 181 sheet: -1.56 (0.91), residues: 38 loop : -1.12 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.016 0.001 PHE A1014 TYR 0.020 0.001 TYR A1109 ARG 0.003 0.000 ARG B2257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1320.29 seconds wall clock time: 24 minutes 21.74 seconds (1461.74 seconds total)