Starting phenix.real_space_refine on Thu Dec 7 21:16:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/12_2023/7p2q_13172_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/12_2023/7p2q_13172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/12_2023/7p2q_13172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/12_2023/7p2q_13172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/12_2023/7p2q_13172_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/12_2023/7p2q_13172_neut.pdb" } resolution = 4.9 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3106 2.51 5 N 778 2.21 5 O 873 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-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4780 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain: "B" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1426 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "C" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1411 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "D" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 696 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.18, per 1000 atoms: 0.67 Number of scatterers: 4780 At special positions: 0 Unit cell: (81.81, 84.24, 126.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 873 8.00 N 778 7.00 C 3106 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 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN B 141 " Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 821.5 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 6 sheets defined 41.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 26 through 56 removed outlier: 4.288A pdb=" N LEU A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.782A pdb=" N VAL A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 33 Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 79 through 105 Processing helix chain 'C' and resid 106 through 109 removed outlier: 3.516A pdb=" N GLU C 109 " --> pdb=" O PRO C 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 106 through 109' Processing helix chain 'C' and resid 110 through 136 removed outlier: 3.720A pdb=" N LEU C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 207 through 224 removed outlier: 3.700A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.653A pdb=" N LEU D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 109 Processing helix chain 'D' and resid 112 through 131 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.601A pdb=" N LEU D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 3.983A pdb=" N ASP A 77 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99 removed outlier: 5.282A pdb=" N VAL A 110 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS A 126 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 112 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.094A pdb=" N VAL B 51 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 63 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP B 53 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER B 61 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 129 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.679A pdb=" N GLN B 84 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 104 Processing sheet with id=AA6, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.622A pdb=" N LEU C 159 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C 142 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TRP C 157 " --> pdb=" O VAL C 142 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 693 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1460 1.34 - 1.46: 971 1.46 - 1.58: 2424 1.58 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 4896 Sorted by residual: bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.567 -0.048 2.00e-02 2.50e+03 5.76e+00 bond pdb=" C1 MAN E 4 " pdb=" C2 MAN E 4 " ideal model delta sigma weight residual 1.526 1.563 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" C1 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sigma weight residual 1.410 1.445 -0.035 2.00e-02 2.50e+03 2.99e+00 bond pdb=" C5 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.418 1.452 -0.034 2.00e-02 2.50e+03 2.94e+00 bond pdb=" C LEU D 131 " pdb=" N PRO D 132 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.18e-02 7.18e+03 2.88e+00 ... (remaining 4891 not shown) Histogram of bond angle deviations from ideal: 100.72 - 107.41: 182 107.41 - 114.10: 2765 114.10 - 120.79: 2047 120.79 - 127.48: 1585 127.48 - 134.17: 50 Bond angle restraints: 6629 Sorted by residual: angle pdb=" C LYS B 121 " pdb=" N ASP B 122 " pdb=" CA ASP B 122 " ideal model delta sigma weight residual 121.54 131.00 -9.46 1.91e+00 2.74e-01 2.45e+01 angle pdb=" C GLY B 133 " pdb=" N ASN B 134 " pdb=" CA ASN B 134 " ideal model delta sigma weight residual 121.54 130.70 -9.16 1.91e+00 2.74e-01 2.30e+01 angle pdb=" C GLU A 58 " pdb=" N SER A 59 " pdb=" CA SER A 59 " ideal model delta sigma weight residual 121.80 130.19 -8.39 2.44e+00 1.68e-01 1.18e+01 angle pdb=" N SER A 59 " pdb=" CA SER A 59 " pdb=" C SER A 59 " ideal model delta sigma weight residual 109.81 116.82 -7.01 2.21e+00 2.05e-01 1.00e+01 angle pdb=" CA LEU D 75 " pdb=" CB LEU D 75 " pdb=" CG LEU D 75 " ideal model delta sigma weight residual 116.30 125.83 -9.53 3.50e+00 8.16e-02 7.42e+00 ... (remaining 6624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.01: 2764 14.01 - 28.02: 104 28.02 - 42.03: 38 42.03 - 56.04: 2 56.04 - 70.05: 3 Dihedral angle restraints: 2911 sinusoidal: 1203 harmonic: 1708 Sorted by residual: dihedral pdb=" CA ASP C 154 " pdb=" C ASP C 154 " pdb=" N ASP C 155 " pdb=" CA ASP C 155 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA TYR B 174 " pdb=" C TYR B 174 " pdb=" N GLU B 175 " pdb=" CA GLU B 175 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER D 74 " pdb=" C SER D 74 " pdb=" N LEU D 75 " pdb=" CA LEU D 75 " ideal model delta harmonic sigma weight residual -180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 2908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 590 0.057 - 0.114: 138 0.114 - 0.171: 22 0.171 - 0.228: 5 0.228 - 0.285: 1 Chirality restraints: 756 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE B 109 " pdb=" CA ILE B 109 " pdb=" CG1 ILE B 109 " pdb=" CG2 ILE B 109 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN B 134 " pdb=" N ASN B 134 " pdb=" C ASN B 134 " pdb=" CB ASN B 134 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 753 not shown) Planarity restraints: 822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 140 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO D 141 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 70 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 71 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 37 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 38 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " -0.026 5.00e-02 4.00e+02 ... (remaining 819 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1005 2.79 - 3.32: 4108 3.32 - 3.85: 7306 3.85 - 4.37: 7850 4.37 - 4.90: 13680 Nonbonded interactions: 33949 Sorted by model distance: nonbonded pdb=" NH1 ARG A 109 " pdb=" CE1 PHE B 86 " model vdw 2.264 3.420 nonbonded pdb=" O LYS B 121 " pdb=" OD1 ASP B 122 " model vdw 2.290 3.040 nonbonded pdb=" NH1 ARG C 84 " pdb=" OE2 GLU C 136 " model vdw 2.352 2.520 nonbonded pdb=" OG SER B 90 " pdb=" O THR B 145 " model vdw 2.357 2.440 nonbonded pdb=" OD1 ASP A 120 " pdb=" NZ LYS A 147 " model vdw 2.401 2.520 ... (remaining 33944 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: 0.330 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: 1.850 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 16.620 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 0.048 4896 Z= 0.243 Angle : 0.840 9.532 6629 Z= 0.432 Chirality : 0.051 0.285 756 Planarity : 0.007 0.057 821 Dihedral : 9.062 70.055 1809 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.29), residues: 579 helix: -1.26 (0.24), residues: 220 sheet: -1.18 (0.47), residues: 120 loop : -3.26 (0.32), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 157 HIS 0.009 0.002 HIS C 144 PHE 0.024 0.002 PHE A 80 TYR 0.023 0.002 TYR B 174 ARG 0.005 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2131 time to fit residues: 68.2344 Evaluate side-chains 146 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4896 Z= 0.246 Angle : 0.714 7.543 6629 Z= 0.364 Chirality : 0.044 0.180 756 Planarity : 0.006 0.083 821 Dihedral : 6.693 57.614 674 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.19 % Allowed : 1.92 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.33), residues: 579 helix: 0.67 (0.32), residues: 225 sheet: -0.70 (0.49), residues: 126 loop : -2.74 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 101 HIS 0.004 0.001 HIS C 144 PHE 0.019 0.002 PHE A 37 TYR 0.023 0.002 TYR A 32 ARG 0.009 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 181 average time/residue: 0.1829 time to fit residues: 40.7162 Evaluate side-chains 128 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.587 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0462 time to fit residues: 0.8608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4896 Z= 0.193 Angle : 0.669 6.977 6629 Z= 0.336 Chirality : 0.043 0.202 756 Planarity : 0.005 0.051 821 Dihedral : 6.470 55.393 674 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.19 % Allowed : 2.30 % Favored : 97.50 % 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: -0.74 (0.35), residues: 579 helix: 1.34 (0.33), residues: 225 sheet: -0.25 (0.49), residues: 131 loop : -2.65 (0.35), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 148 HIS 0.004 0.001 HIS C 216 PHE 0.015 0.001 PHE A 37 TYR 0.029 0.002 TYR C 121 ARG 0.004 0.001 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 179 average time/residue: 0.1772 time to fit residues: 39.3188 Evaluate side-chains 136 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0457 time to fit residues: 0.8430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 48 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.6022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4896 Z= 0.181 Angle : 0.660 8.093 6629 Z= 0.330 Chirality : 0.043 0.185 756 Planarity : 0.004 0.043 821 Dihedral : 6.235 55.610 674 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: -0.51 (0.35), residues: 579 helix: 1.54 (0.34), residues: 225 sheet: -0.28 (0.49), residues: 135 loop : -2.47 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 148 HIS 0.003 0.001 HIS C 216 PHE 0.023 0.002 PHE A 80 TYR 0.019 0.002 TYR C 121 ARG 0.003 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1684 time to fit residues: 36.8151 Evaluate side-chains 136 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.565 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 0.0270 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 overall best weight: 3.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS A 129 ASN A 143 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.6698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4896 Z= 0.251 Angle : 0.721 7.969 6629 Z= 0.357 Chirality : 0.043 0.169 756 Planarity : 0.004 0.044 821 Dihedral : 6.145 55.384 674 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: -0.44 (0.35), residues: 579 helix: 1.72 (0.35), residues: 221 sheet: 0.12 (0.54), residues: 105 loop : -2.46 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 148 HIS 0.005 0.001 HIS C 216 PHE 0.014 0.002 PHE A 84 TYR 0.019 0.002 TYR C 121 ARG 0.005 0.001 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1690 time to fit residues: 34.4446 Evaluate side-chains 128 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 8.9990 chunk 54 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.7137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4896 Z= 0.253 Angle : 0.712 8.450 6629 Z= 0.360 Chirality : 0.044 0.170 756 Planarity : 0.005 0.044 821 Dihedral : 6.123 55.482 674 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: -0.45 (0.35), residues: 579 helix: 1.60 (0.34), residues: 222 sheet: -0.27 (0.49), residues: 130 loop : -2.32 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 144 HIS 0.005 0.001 HIS C 216 PHE 0.016 0.002 PHE B 14 TYR 0.023 0.002 TYR B 88 ARG 0.007 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1736 time to fit residues: 36.5305 Evaluate side-chains 126 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.7432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4896 Z= 0.217 Angle : 0.700 8.386 6629 Z= 0.350 Chirality : 0.043 0.151 756 Planarity : 0.004 0.044 821 Dihedral : 6.056 55.520 674 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -0.47 (0.35), residues: 579 helix: 1.68 (0.35), residues: 222 sheet: -0.35 (0.48), residues: 130 loop : -2.42 (0.36), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 148 HIS 0.004 0.001 HIS C 216 PHE 0.019 0.002 PHE C 197 TYR 0.019 0.002 TYR C 170 ARG 0.004 0.001 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1684 time to fit residues: 33.6984 Evaluate side-chains 124 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.462 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.7613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4896 Z= 0.185 Angle : 0.686 8.959 6629 Z= 0.339 Chirality : 0.043 0.191 756 Planarity : 0.004 0.042 821 Dihedral : 5.930 55.752 674 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.48 (0.35), residues: 579 helix: 1.70 (0.34), residues: 221 sheet: -0.38 (0.47), residues: 130 loop : -2.41 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 148 HIS 0.012 0.002 HIS D 71 PHE 0.024 0.002 PHE C 197 TYR 0.012 0.001 TYR C 170 ARG 0.004 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1671 time to fit residues: 32.6419 Evaluate side-chains 120 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.586 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.7888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4896 Z= 0.230 Angle : 0.722 8.797 6629 Z= 0.363 Chirality : 0.044 0.186 756 Planarity : 0.004 0.041 821 Dihedral : 5.978 55.462 674 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.54 (0.35), residues: 579 helix: 1.62 (0.34), residues: 221 sheet: -0.19 (0.48), residues: 124 loop : -2.51 (0.35), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 144 HIS 0.010 0.002 HIS D 71 PHE 0.021 0.002 PHE C 197 TYR 0.012 0.002 TYR C 170 ARG 0.008 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1701 time to fit residues: 33.2707 Evaluate side-chains 121 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.601 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 35 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.0470 chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 0.0970 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.7851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4896 Z= 0.164 Angle : 0.710 9.735 6629 Z= 0.349 Chirality : 0.044 0.172 756 Planarity : 0.004 0.038 821 Dihedral : 5.802 55.875 674 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.35), residues: 579 helix: 1.66 (0.35), residues: 221 sheet: 0.00 (0.49), residues: 121 loop : -2.51 (0.35), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 148 HIS 0.004 0.001 HIS C 199 PHE 0.015 0.002 PHE C 166 TYR 0.016 0.001 TYR C 170 ARG 0.005 0.001 ARG A 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1682 time to fit residues: 34.6846 Evaluate side-chains 119 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.074160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059113 restraints weight = 29274.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060497 restraints weight = 23116.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.061567 restraints weight = 19245.548| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.7906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4896 Z= 0.169 Angle : 0.716 9.559 6629 Z= 0.355 Chirality : 0.044 0.167 756 Planarity : 0.004 0.036 821 Dihedral : 5.726 55.871 674 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.58 (0.35), residues: 579 helix: 1.49 (0.35), residues: 221 sheet: 0.10 (0.53), residues: 111 loop : -2.51 (0.34), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 157 HIS 0.010 0.001 HIS D 71 PHE 0.012 0.001 PHE A 37 TYR 0.018 0.001 TYR D 81 ARG 0.004 0.000 ARG C 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1399.88 seconds wall clock time: 25 minutes 51.20 seconds (1551.20 seconds total)