Sun 23 Dec 22:23:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2aj6-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aj6-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aj6-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-1.9-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-1.9-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:14 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-1.9-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 130 and 0 Target number of residues in the AU: 130 Target solvent content: 0.4824 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 159 Adjusted target solvent content: 0.37 Input MTZ file: 2aj6-1.9-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 23 Cell parameters: 40.044 74.871 90.673 90.000 90.000 90.000 Input sequence file: 2aj6-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 1272 target number of atoms Had to go as low as 0.25 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 28.866 1.900 Wilson plot Bfac: 19.60 11093 reflections ( 99.75 % complete ) and 0 restraints for refining 1408 atoms. Observations/parameters ratio is 1.97 ------------------------------------------------------ Starting model: R = 0.3112 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2530 (Rfree = 0.000) for 1408 atoms. Found 46 (55 requested) and removed 47 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.88 2.24 Round 1: 97 peptides, 7 chains. Longest chain 23 peptides. Score 0.818 Round 2: 112 peptides, 2 chains. Longest chain 104 peptides. Score 0.941 Round 3: 111 peptides, 2 chains. Longest chain 66 peptides. Score 0.939 Round 4: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Round 5: 111 peptides, 2 chains. Longest chain 71 peptides. Score 0.939 Taking the results from Round 4 Chains 1, Residues 112, Estimated correctness of the model 99.8 % 1 chains (112 residues) have been docked in sequence ------------------------------------------------------ 11093 reflections ( 99.75 % complete ) and 1275 restraints for refining 1243 atoms. 330 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2768 (Rfree = 0.000) for 1243 atoms. Found 32 (49 requested) and removed 29 (24 requested) atoms. Cycle 2: After refmac, R = 0.2535 (Rfree = 0.000) for 1234 atoms. Found 30 (48 requested) and removed 24 (24 requested) atoms. Cycle 3: After refmac, R = 0.2276 (Rfree = 0.000) for 1235 atoms. Found 25 (47 requested) and removed 24 (24 requested) atoms. Cycle 4: After refmac, R = 0.2132 (Rfree = 0.000) for 1232 atoms. Found 36 (45 requested) and removed 24 (24 requested) atoms. Cycle 5: After refmac, R = 0.2083 (Rfree = 0.000) for 1241 atoms. Found 21 (45 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.88 2.24 Round 1: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Round 2: 111 peptides, 3 chains. Longest chain 70 peptides. Score 0.927 Round 3: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Round 4: 111 peptides, 3 chains. Longest chain 68 peptides. Score 0.927 Round 5: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Taking the results from Round 5 Chains 1, Residues 112, Estimated correctness of the model 99.8 % 1 chains (112 residues) have been docked in sequence ------------------------------------------------------ 11093 reflections ( 99.75 % complete ) and 1225 restraints for refining 1236 atoms. 280 conditional restraints added. Observations/parameters ratio is 2.24 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2167 (Rfree = 0.000) for 1236 atoms. Found 30 (44 requested) and removed 27 (24 requested) atoms. Cycle 7: After refmac, R = 0.2032 (Rfree = 0.000) for 1233 atoms. Found 20 (43 requested) and removed 25 (24 requested) atoms. Cycle 8: After refmac, R = 0.1963 (Rfree = 0.000) for 1227 atoms. Found 28 (41 requested) and removed 25 (24 requested) atoms. Cycle 9: After refmac, R = 0.1923 (Rfree = 0.000) for 1229 atoms. Found 23 (40 requested) and removed 24 (24 requested) atoms. Cycle 10: After refmac, R = 0.1895 (Rfree = 0.000) for 1227 atoms. Found 29 (39 requested) and removed 20 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.90 2.27 Round 1: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Round 2: 112 peptides, 2 chains. Longest chain 77 peptides. Score 0.941 Round 3: 111 peptides, 2 chains. Longest chain 68 peptides. Score 0.939 Round 4: 109 peptides, 3 chains. Longest chain 64 peptides. Score 0.923 Round 5: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Taking the results from Round 5 Chains 1, Residues 112, Estimated correctness of the model 99.8 % 1 chains (112 residues) have been docked in sequence ------------------------------------------------------ 11093 reflections ( 99.75 % complete ) and 1218 restraints for refining 1233 atoms. 273 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2086 (Rfree = 0.000) for 1233 atoms. Found 34 (38 requested) and removed 28 (24 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1941 (Rfree = 0.000) for 1239 atoms. Found 20 (38 requested) and removed 24 (24 requested) atoms. Cycle 13: After refmac, R = 0.1883 (Rfree = 0.000) for 1234 atoms. Found 28 (36 requested) and removed 21 (24 requested) atoms. Cycle 14: After refmac, R = 0.1810 (Rfree = 0.000) for 1241 atoms. Found 21 (36 requested) and removed 17 (24 requested) atoms. Cycle 15: After refmac, R = 0.1806 (Rfree = 0.000) for 1245 atoms. Found 29 (35 requested) and removed 16 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.89 2.26 Round 1: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Round 2: 112 peptides, 3 chains. Longest chain 71 peptides. Score 0.929 Round 3: 114 peptides, 2 chains. Longest chain 68 peptides. Score 0.944 Round 4: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Round 5: 110 peptides, 3 chains. Longest chain 68 peptides. Score 0.925 Taking the results from Round 4 Chains 1, Residues 112, Estimated correctness of the model 99.8 % 1 chains (112 residues) have been docked in sequence ------------------------------------------------------ 11093 reflections ( 99.75 % complete ) and 1204 restraints for refining 1244 atoms. 259 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1977 (Rfree = 0.000) for 1244 atoms. Found 31 (34 requested) and removed 31 (24 requested) atoms. Cycle 17: After refmac, R = 0.1846 (Rfree = 0.000) for 1244 atoms. Found 30 (33 requested) and removed 17 (24 requested) atoms. Cycle 18: After refmac, R = 0.1818 (Rfree = 0.000) for 1257 atoms. Found 23 (32 requested) and removed 24 (24 requested) atoms. Cycle 19: After refmac, R = 0.1795 (Rfree = 0.000) for 1253 atoms. Found 28 (31 requested) and removed 22 (24 requested) atoms. Cycle 20: After refmac, R = 0.1788 (Rfree = 0.000) for 1259 atoms. Found 23 (30 requested) and removed 23 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.90 2.27 Round 1: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Round 2: 114 peptides, 2 chains. Longest chain 68 peptides. Score 0.944 Round 3: 112 peptides, 3 chains. Longest chain 71 peptides. Score 0.929 Round 4: 114 peptides, 1 chains. Longest chain 114 peptides. Score 0.955 Round 5: 114 peptides, 2 chains. Longest chain 68 peptides. Score 0.944 Taking the results from Round 4 Chains 1, Residues 113, Estimated correctness of the model 99.8 % 1 chains (113 residues) have been docked in sequence ------------------------------------------------------ 11093 reflections ( 99.75 % complete ) and 1224 restraints for refining 1244 atoms. 270 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2000 (Rfree = 0.000) for 1244 atoms. Found 29 (29 requested) and removed 29 (24 requested) atoms. Cycle 22: After refmac, R = 0.1884 (Rfree = 0.000) for 1243 atoms. Found 25 (28 requested) and removed 21 (24 requested) atoms. Cycle 23: After refmac, R = 0.1836 (Rfree = 0.000) for 1247 atoms. Found 22 (27 requested) and removed 16 (24 requested) atoms. Cycle 24: After refmac, R = 0.1785 (Rfree = 0.000) for 1252 atoms. Found 26 (26 requested) and removed 21 (24 requested) atoms. Cycle 25: After refmac, R = 0.1792 (Rfree = 0.000) for 1255 atoms. Found 25 (25 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.89 2.26 Round 1: 114 peptides, 1 chains. Longest chain 114 peptides. Score 0.955 Round 2: 114 peptides, 1 chains. Longest chain 114 peptides. Score 0.955 Round 3: 113 peptides, 2 chains. Longest chain 78 peptides. Score 0.942 Round 4: 111 peptides, 2 chains. Longest chain 68 peptides. Score 0.939 Round 5: 114 peptides, 1 chains. Longest chain 114 peptides. Score 0.955 Taking the results from Round 5 Chains 1, Residues 113, Estimated correctness of the model 99.8 % 1 chains (113 residues) have been docked in sequence ------------------------------------------------------ 11093 reflections ( 99.75 % complete ) and 1206 restraints for refining 1244 atoms. 252 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1945 (Rfree = 0.000) for 1244 atoms. Found 24 (24 requested) and removed 27 (24 requested) atoms. Cycle 27: After refmac, R = 0.1822 (Rfree = 0.000) for 1241 atoms. Found 22 (24 requested) and removed 10 (24 requested) atoms. Cycle 28: After refmac, R = 0.1765 (Rfree = 0.000) for 1253 atoms. Found 24 (24 requested) and removed 13 (24 requested) atoms. Cycle 29: After refmac, R = 0.1740 (Rfree = 0.000) for 1263 atoms. Found 24 (24 requested) and removed 15 (24 requested) atoms. Cycle 30: After refmac, R = 0.1725 (Rfree = 0.000) for 1270 atoms. Found 19 (25 requested) and removed 19 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.90 2.27 Round 1: 114 peptides, 1 chains. Longest chain 114 peptides. Score 0.955 Round 2: 113 peptides, 3 chains. Longest chain 68 peptides. Score 0.930 Round 3: 113 peptides, 2 chains. Longest chain 71 peptides. Score 0.942 Round 4: 114 peptides, 2 chains. Longest chain 68 peptides. Score 0.944 Round 5: 113 peptides, 2 chains. Longest chain 78 peptides. Score 0.942 Taking the results from Round 1 Chains 1, Residues 113, Estimated correctness of the model 99.8 % 1 chains (113 residues) have been docked in sequence ------------------------------------------------------ 11093 reflections ( 99.75 % complete ) and 1215 restraints for refining 1244 atoms. 261 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1947 (Rfree = 0.000) for 1244 atoms. Found 24 (24 requested) and removed 26 (24 requested) atoms. Cycle 32: After refmac, R = 0.1823 (Rfree = 0.000) for 1242 atoms. Found 24 (24 requested) and removed 11 (24 requested) atoms. Cycle 33: After refmac, R = 0.1768 (Rfree = 0.000) for 1252 atoms. Found 21 (24 requested) and removed 12 (24 requested) atoms. Cycle 34: After refmac, R = 0.1738 (Rfree = 0.000) for 1259 atoms. Found 20 (24 requested) and removed 13 (24 requested) atoms. Cycle 35: After refmac, R = 0.1707 (Rfree = 0.000) for 1264 atoms. Found 19 (25 requested) and removed 15 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.89 2.26 Round 1: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Round 2: 112 peptides, 3 chains. Longest chain 67 peptides. Score 0.929 Round 3: 112 peptides, 2 chains. Longest chain 70 peptides. Score 0.941 Round 4: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Round 5: 112 peptides, 3 chains. Longest chain 67 peptides. Score 0.929 Taking the results from Round 4 Chains 1, Residues 112, Estimated correctness of the model 99.8 % 1 chains (112 residues) have been docked in sequence ------------------------------------------------------ 11093 reflections ( 99.75 % complete ) and 1233 restraints for refining 1244 atoms. 288 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1926 (Rfree = 0.000) for 1244 atoms. Found 24 (24 requested) and removed 28 (24 requested) atoms. Cycle 37: After refmac, R = 0.1810 (Rfree = 0.000) for 1239 atoms. Found 18 (24 requested) and removed 12 (24 requested) atoms. Cycle 38: After refmac, R = 0.1751 (Rfree = 0.000) for 1241 atoms. Found 24 (24 requested) and removed 14 (24 requested) atoms. Cycle 39: After refmac, R = 0.1712 (Rfree = 0.000) for 1249 atoms. Found 19 (24 requested) and removed 14 (24 requested) atoms. Cycle 40: After refmac, R = 0.1727 (Rfree = 0.000) for 1253 atoms. Found 23 (24 requested) and removed 14 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.88 2.24 Round 1: 112 peptides, 1 chains. Longest chain 112 peptides. Score 0.952 Round 2: 112 peptides, 1 chains. Longest chain 112 peptides. Score 0.952 Round 3: 110 peptides, 3 chains. Longest chain 69 peptides. Score 0.925 Round 4: 112 peptides, 2 chains. Longest chain 66 peptides. Score 0.941 Round 5: 112 peptides, 1 chains. Longest chain 112 peptides. Score 0.952 Taking the results from Round 5 Chains 1, Residues 111, Estimated correctness of the model 99.8 % 1 chains (111 residues) have been docked in sequence ------------------------------------------------------ 11093 reflections ( 99.75 % complete ) and 1230 restraints for refining 1244 atoms. 290 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1948 (Rfree = 0.000) for 1244 atoms. Found 24 (24 requested) and removed 23 (24 requested) atoms. Cycle 42: After refmac, R = 0.1831 (Rfree = 0.000) for 1245 atoms. Found 21 (24 requested) and removed 21 (24 requested) atoms. Cycle 43: After refmac, R = 0.1782 (Rfree = 0.000) for 1243 atoms. Found 24 (24 requested) and removed 18 (24 requested) atoms. Cycle 44: After refmac, R = 0.1749 (Rfree = 0.000) for 1247 atoms. Found 24 (24 requested) and removed 11 (24 requested) atoms. Cycle 45: After refmac, R = 0.1720 (Rfree = 0.000) for 1260 atoms. Found 16 (24 requested) and removed 17 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.88 2.24 Round 1: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Round 2: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Round 3: 109 peptides, 3 chains. Longest chain 66 peptides. Score 0.923 Round 4: 113 peptides, 1 chains. Longest chain 113 peptides. Score 0.954 Round 5: 111 peptides, 3 chains. Longest chain 62 peptides. Score 0.927 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 1, Residues 112, Estimated correctness of the model 99.8 % 1 chains (112 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 11093 reflections ( 99.75 % complete ) and 951 restraints for refining 933 atoms. Observations/parameters ratio is 2.97 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2672 (Rfree = 0.000) for 933 atoms. Found 18 (18 requested) and removed 0 (18 requested) atoms. Cycle 47: After refmac, R = 0.2487 (Rfree = 0.000) for 933 atoms. Found 14 (18 requested) and removed 0 (18 requested) atoms. Cycle 48: After refmac, R = 0.2346 (Rfree = 0.000) for 933 atoms. Found 11 (19 requested) and removed 1 (19 requested) atoms. Cycle 49: After refmac, R = 0.2265 (Rfree = 0.000) for 933 atoms. Found 4 (19 requested) and removed 1 (19 requested) atoms. TimeTaking 28.08