null Sun 23 Dec 22:23:14 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 2pn2-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pn2-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pn2-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-3.8-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/2pn2-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-3.8-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 22:23:22 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/2pn2-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-3.8-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 85 and 0 Target number of residues in the AU: 85 Target solvent content: 0.6731 Checking the provided sequence file Detected sequence length: 155 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 155 Adjusted target solvent content: 0.40 Input MTZ file: 2pn2-3.8-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: 20 Cell parameters: 47.282 57.586 103.372 90.000 90.000 90.000 Input sequence file: 2pn2-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1240 target number of atoms Had to go as low as 0.50 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 3 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: 51.686 3.800 Wilson plot Bfac: 92.96 1503 reflections ( 98.82 % complete ) and 0 restraints for refining 1380 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3451 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3101 (Rfree = 0.000) for 1380 atoms. Found 5 (7 requested) and removed 15 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 4.19 Search for helices and strands: 0 residues in 0 chains, 1385 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 6 peptides. Score 0.288 Round 2: 68 peptides, 10 chains. Longest chain 15 peptides. Score 0.504 Round 3: 75 peptides, 11 chains. Longest chain 11 peptides. Score 0.529 Round 4: 71 peptides, 9 chains. Longest chain 17 peptides. Score 0.575 Round 5: 69 peptides, 9 chains. Longest chain 17 peptides. Score 0.556 Taking the results from Round 4 Chains 9, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1503 reflections ( 98.82 % complete ) and 2812 restraints for refining 1121 atoms. 2573 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2428 (Rfree = 0.000) for 1121 atoms. Found 3 (6 requested) and removed 12 (3 requested) atoms. Cycle 2: After refmac, R = 0.2292 (Rfree = 0.000) for 1087 atoms. Found 3 (6 requested) and removed 9 (3 requested) atoms. Cycle 3: After refmac, R = 0.2268 (Rfree = 0.000) for 1078 atoms. Found 2 (5 requested) and removed 7 (2 requested) atoms. Cycle 4: After refmac, R = 0.1978 (Rfree = 0.000) for 1070 atoms. Found 1 (5 requested) and removed 5 (2 requested) atoms. Cycle 5: After refmac, R = 0.2011 (Rfree = 0.000) for 1065 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 4.25 Search for helices and strands: 0 residues in 0 chains, 1112 seeds are put forward Round 1: 57 peptides, 11 chains. Longest chain 10 peptides. Score 0.335 Round 2: 63 peptides, 11 chains. Longest chain 10 peptides. Score 0.405 Round 3: 63 peptides, 10 chains. Longest chain 12 peptides. Score 0.452 Round 4: 68 peptides, 11 chains. Longest chain 13 peptides. Score 0.459 Round 5: 75 peptides, 11 chains. Longest chain 19 peptides. Score 0.529 Taking the results from Round 5 Chains 12, Residues 64, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1503 reflections ( 98.82 % complete ) and 2346 restraints for refining 1043 atoms. 2072 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2322 (Rfree = 0.000) for 1043 atoms. Found 2 (5 requested) and removed 16 (2 requested) atoms. Cycle 7: After refmac, R = 0.2486 (Rfree = 0.000) for 1021 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 8: After refmac, R = 0.1986 (Rfree = 0.000) for 1010 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. Cycle 9: After refmac, R = 0.1983 (Rfree = 0.000) for 1004 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. Cycle 10: After refmac, R = 0.2353 (Rfree = 0.000) for 1000 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 4.21 Search for helices and strands: 0 residues in 0 chains, 1023 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 10 peptides. Score 0.309 Round 2: 72 peptides, 13 chains. Longest chain 15 peptides. Score 0.410 Round 3: 73 peptides, 12 chains. Longest chain 9 peptides. Score 0.467 Round 4: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.359 Round 5: 62 peptides, 9 chains. Longest chain 11 peptides. Score 0.488 Taking the results from Round 5 Chains 9, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1503 reflections ( 98.82 % complete ) and 2504 restraints for refining 1033 atoms. 2301 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1945 (Rfree = 0.000) for 1033 atoms. Found 1 (5 requested) and removed 12 (2 requested) atoms. Cycle 12: After refmac, R = 0.1855 (Rfree = 0.000) for 1018 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 13: After refmac, R = 0.1811 (Rfree = 0.000) for 1011 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 14: After refmac, R = 0.1794 (Rfree = 0.000) for 1006 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.1692 (Rfree = 0.000) for 1003 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.66 4.19 Search for helices and strands: 0 residues in 0 chains, 1032 seeds are put forward Round 1: 65 peptides, 11 chains. Longest chain 15 peptides. Score 0.427 Round 2: 55 peptides, 9 chains. Longest chain 9 peptides. Score 0.412 Round 3: 59 peptides, 8 chains. Longest chain 16 peptides. Score 0.503 Round 4: 58 peptides, 9 chains. Longest chain 13 peptides. Score 0.446 Round 5: 65 peptides, 10 chains. Longest chain 16 peptides. Score 0.474 Taking the results from Round 3 Chains 8, Residues 51, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 1503 reflections ( 98.82 % complete ) and 2275 restraints for refining 1018 atoms. 2028 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2051 (Rfree = 0.000) for 1018 atoms. Found 3 (5 requested) and removed 15 (2 requested) atoms. Cycle 17: After refmac, R = 0.1813 (Rfree = 0.000) for 1000 atoms. Found 2 (5 requested) and removed 8 (2 requested) atoms. Cycle 18: After refmac, R = 0.1772 (Rfree = 0.000) for 993 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 19: After refmac, R = 0.1720 (Rfree = 0.000) for 989 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 20: After refmac, R = 0.1689 (Rfree = 0.000) for 986 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.77 4.31 Search for helices and strands: 0 residues in 0 chains, 1019 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.263 Round 2: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.408 Round 3: 56 peptides, 8 chains. Longest chain 11 peptides. Score 0.472 Round 4: 59 peptides, 10 chains. Longest chain 9 peptides. Score 0.408 Round 5: 57 peptides, 8 chains. Longest chain 11 peptides. Score 0.483 Taking the results from Round 5 Chains 8, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1503 reflections ( 98.82 % complete ) and 2389 restraints for refining 1018 atoms. 2201 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1857 (Rfree = 0.000) for 1018 atoms. Found 0 (5 requested) and removed 10 (2 requested) atoms. Cycle 22: After refmac, R = 0.1704 (Rfree = 0.000) for 1004 atoms. Found 0 (5 requested) and removed 5 (2 requested) atoms. Cycle 23: After refmac, R = 0.1660 (Rfree = 0.000) for 998 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.1624 (Rfree = 0.000) for 992 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.1568 (Rfree = 0.000) for 991 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 4.29 Search for helices and strands: 0 residues in 0 chains, 1029 seeds are put forward Round 1: 53 peptides, 9 chains. Longest chain 10 peptides. Score 0.389 Round 2: 64 peptides, 8 chains. Longest chain 12 peptides. Score 0.552 Round 3: 70 peptides, 10 chains. Longest chain 13 peptides. Score 0.524 Round 4: 71 peptides, 9 chains. Longest chain 13 peptides. Score 0.575 Round 5: 64 peptides, 8 chains. Longest chain 13 peptides. Score 0.552 Taking the results from Round 4 Chains 9, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1503 reflections ( 98.82 % complete ) and 2297 restraints for refining 1046 atoms. 2058 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1935 (Rfree = 0.000) for 1046 atoms. Found 3 (5 requested) and removed 9 (2 requested) atoms. Cycle 27: After refmac, R = 0.1694 (Rfree = 0.000) for 1037 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 28: After refmac, R = 0.1611 (Rfree = 0.000) for 1034 atoms. Found 0 (5 requested) and removed 5 (2 requested) atoms. Cycle 29: After refmac, R = 0.1706 (Rfree = 0.000) for 1028 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.1826 (Rfree = 0.000) for 1022 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 4.30 Search for helices and strands: 0 residues in 0 chains, 1048 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.248 Round 2: 58 peptides, 11 chains. Longest chain 7 peptides. Score 0.347 Round 3: 54 peptides, 10 chains. Longest chain 10 peptides. Score 0.350 Round 4: 66 peptides, 10 chains. Longest chain 13 peptides. Score 0.484 Round 5: 70 peptides, 10 chains. Longest chain 21 peptides. Score 0.524 Taking the results from Round 5 Chains 11, Residues 60, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1503 reflections ( 98.82 % complete ) and 2449 restraints for refining 1094 atoms. 2188 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2221 (Rfree = 0.000) for 1094 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 32: After refmac, R = 0.1927 (Rfree = 0.000) for 1087 atoms. Found 2 (5 requested) and removed 7 (2 requested) atoms. Cycle 33: After refmac, R = 0.1878 (Rfree = 0.000) for 1080 atoms. Found 1 (5 requested) and removed 7 (2 requested) atoms. Cycle 34: After refmac, R = 0.1928 (Rfree = 0.000) for 1072 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.1773 (Rfree = 0.000) for 1069 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 4.26 Search for helices and strands: 0 residues in 0 chains, 1130 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.299 Round 2: 58 peptides, 9 chains. Longest chain 9 peptides. Score 0.446 Round 3: 50 peptides, 9 chains. Longest chain 9 peptides. Score 0.354 Round 4: 56 peptides, 9 chains. Longest chain 10 peptides. Score 0.424 Round 5: 49 peptides, 8 chains. Longest chain 10 peptides. Score 0.394 Taking the results from Round 2 Chains 9, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1503 reflections ( 98.82 % complete ) and 2621 restraints for refining 1083 atoms. 2434 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1965 (Rfree = 0.000) for 1083 atoms. Found 5 (5 requested) and removed 25 (2 requested) atoms. Cycle 37: After refmac, R = 0.1755 (Rfree = 0.000) for 1058 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. Cycle 38: After refmac, R = 0.1653 (Rfree = 0.000) for 1053 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.1608 (Rfree = 0.000) for 1051 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.1587 (Rfree = 0.000) for 1047 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 4.25 Search for helices and strands: 0 residues in 0 chains, 1077 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.261 Round 2: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.350 Round 3: 53 peptides, 10 chains. Longest chain 7 peptides. Score 0.338 Round 4: 60 peptides, 11 chains. Longest chain 10 peptides. Score 0.371 Round 5: 55 peptides, 10 chains. Longest chain 10 peptides. Score 0.362 Taking the results from Round 4 Chains 11, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1503 reflections ( 98.82 % complete ) and 2725 restraints for refining 1088 atoms. 2540 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1967 (Rfree = 0.000) for 1088 atoms. Found 4 (5 requested) and removed 9 (2 requested) atoms. Cycle 42: After refmac, R = 0.1875 (Rfree = 0.000) for 1081 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.1749 (Rfree = 0.000) for 1082 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.1714 (Rfree = 0.000) for 1082 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.1687 (Rfree = 0.000) for 1080 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 4.25 Search for helices and strands: 0 residues in 0 chains, 1114 seeds are put forward Round 1: 39 peptides, 8 chains. Longest chain 8 peptides. Score 0.268 Round 2: 61 peptides, 11 chains. Longest chain 13 peptides. Score 0.382 Round 3: 54 peptides, 10 chains. Longest chain 9 peptides. Score 0.350 Round 4: 61 peptides, 11 chains. Longest chain 10 peptides. Score 0.382 Round 5: 51 peptides, 10 chains. Longest chain 11 peptides. Score 0.314 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2pn2-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1503 reflections ( 98.82 % complete ) and 2640 restraints for refining 1098 atoms. 2451 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1743 (Rfree = 0.000) for 1098 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1634 (Rfree = 0.000) for 1093 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1598 (Rfree = 0.000) for 1090 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.1578 (Rfree = 0.000) for 1088 atoms. Found 0 (5 requested) and removed 1 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:40 GMT 2018 Job finished. TimeTaking 24.43 Used memory is bytes: 5442376