Sun 23 Dec 22:22:46 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 2pn2-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pn2-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pn2-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-3.6-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/2pn2-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-3.6-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 22:22:54 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/2pn2-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-3.6-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 88 and 0 Target number of residues in the AU: 88 Target solvent content: 0.6616 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: 2pn2-3.6-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: 2pn2-3.6-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 3.600 Wilson plot Bfac: 85.60 1760 reflections ( 98.93 % complete ) and 0 restraints for refining 1366 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3373 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3149 (Rfree = 0.000) for 1366 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 4.04 Search for helices and strands: 0 residues in 0 chains, 1383 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 10 peptides. Score 0.347 Round 2: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.427 Round 3: 81 peptides, 11 chains. Longest chain 17 peptides. Score 0.584 Round 4: 85 peptides, 11 chains. Longest chain 15 peptides. Score 0.617 Round 5: 88 peptides, 9 chains. Longest chain 25 peptides. Score 0.706 Taking the results from Round 5 Chains 9, Residues 79, Estimated correctness of the model 51.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1760 reflections ( 98.93 % complete ) and 2550 restraints for refining 1086 atoms. 2243 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2684 (Rfree = 0.000) for 1086 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 2: After refmac, R = 0.2636 (Rfree = 0.000) for 1061 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 3: After refmac, R = 0.2315 (Rfree = 0.000) for 1044 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. Cycle 4: After refmac, R = 0.2267 (Rfree = 0.000) for 1036 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 5: After refmac, R = 0.2350 (Rfree = 0.000) for 1028 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 4.01 Search for helices and strands: 0 residues in 0 chains, 1075 seeds are put forward Round 1: 65 peptides, 9 chains. Longest chain 16 peptides. Score 0.518 Round 2: 60 peptides, 7 chains. Longest chain 14 peptides. Score 0.558 Round 3: 76 peptides, 10 chains. Longest chain 16 peptides. Score 0.579 Round 4: 81 peptides, 11 chains. Longest chain 23 peptides. Score 0.584 Round 5: 77 peptides, 9 chains. Longest chain 20 peptides. Score 0.626 Taking the results from Round 5 Chains 9, Residues 68, Estimated correctness of the model 24.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1760 reflections ( 98.93 % complete ) and 2430 restraints for refining 1037 atoms. 2167 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2671 (Rfree = 0.000) for 1037 atoms. Found 4 (5 requested) and removed 9 (3 requested) atoms. Cycle 7: After refmac, R = 0.2928 (Rfree = 0.000) for 1024 atoms. Found 5 (5 requested) and removed 21 (3 requested) atoms. Cycle 8: After refmac, R = 0.2162 (Rfree = 0.000) for 998 atoms. Found 4 (5 requested) and removed 6 (3 requested) atoms. Cycle 9: After refmac, R = 0.1980 (Rfree = 0.000) for 993 atoms. Found 3 (5 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.1863 (Rfree = 0.000) for 990 atoms. Found 1 (5 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 4.13 Search for helices and strands: 0 residues in 0 chains, 1032 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 10 peptides. Score 0.352 Round 2: 74 peptides, 11 chains. Longest chain 15 peptides. Score 0.520 Round 3: 72 peptides, 11 chains. Longest chain 12 peptides. Score 0.500 Round 4: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.467 Round 5: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.507 Taking the results from Round 2 Chains 11, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1760 reflections ( 98.93 % complete ) and 2207 restraints for refining 984 atoms. 1966 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2244 (Rfree = 0.000) for 984 atoms. Found 5 (5 requested) and removed 6 (3 requested) atoms. Cycle 12: After refmac, R = 0.1954 (Rfree = 0.000) for 981 atoms. Found 3 (5 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.1973 (Rfree = 0.000) for 978 atoms. Found 5 (5 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.1929 (Rfree = 0.000) for 973 atoms. Found 2 (5 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.1707 (Rfree = 0.000) for 970 atoms. Found 2 (5 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 4.17 Search for helices and strands: 0 residues in 0 chains, 997 seeds are put forward Round 1: 63 peptides, 10 chains. Longest chain 13 peptides. Score 0.452 Round 2: 71 peptides, 11 chains. Longest chain 14 peptides. Score 0.490 Round 3: 80 peptides, 11 chains. Longest chain 14 peptides. Score 0.575 Round 4: 78 peptides, 11 chains. Longest chain 14 peptides. Score 0.557 Round 5: 75 peptides, 9 chains. Longest chain 16 peptides. Score 0.609 Taking the results from Round 5 Chains 9, Residues 66, Estimated correctness of the model 18.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1760 reflections ( 98.93 % complete ) and 2194 restraints for refining 987 atoms. 1939 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2382 (Rfree = 0.000) for 987 atoms. Found 5 (5 requested) and removed 10 (3 requested) atoms. Cycle 17: After refmac, R = 0.2047 (Rfree = 0.000) for 979 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. Cycle 18: After refmac, R = 0.1961 (Rfree = 0.000) for 977 atoms. Found 5 (5 requested) and removed 9 (3 requested) atoms. Cycle 19: After refmac, R = 0.1763 (Rfree = 0.000) for 973 atoms. Found 1 (5 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.1704 (Rfree = 0.000) for 970 atoms. Found 3 (5 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 4.06 Search for helices and strands: 0 residues in 0 chains, 999 seeds are put forward Round 1: 60 peptides, 12 chains. Longest chain 9 peptides. Score 0.321 Round 2: 71 peptides, 11 chains. Longest chain 11 peptides. Score 0.490 Round 3: 74 peptides, 12 chains. Longest chain 11 peptides. Score 0.477 Round 4: 76 peptides, 11 chains. Longest chain 14 peptides. Score 0.539 Round 5: 83 peptides, 12 chains. Longest chain 14 peptides. Score 0.563 Taking the results from Round 5 Chains 12, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1760 reflections ( 98.93 % complete ) and 2184 restraints for refining 990 atoms. 1912 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2240 (Rfree = 0.000) for 990 atoms. Found 5 (5 requested) and removed 8 (3 requested) atoms. Cycle 22: After refmac, R = 0.2358 (Rfree = 0.000) for 981 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.2314 (Rfree = 0.000) for 976 atoms. Found 5 (5 requested) and removed 7 (3 requested) atoms. Cycle 24: After refmac, R = 0.1767 (Rfree = 0.000) for 970 atoms. Found 2 (5 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.2103 (Rfree = 0.000) for 967 atoms. Found 5 (5 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 4.03 Search for helices and strands: 0 residues in 0 chains, 1022 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 7 peptides. Score 0.273 Round 2: 66 peptides, 13 chains. Longest chain 9 peptides. Score 0.342 Round 3: 71 peptides, 11 chains. Longest chain 17 peptides. Score 0.490 Round 4: 71 peptides, 12 chains. Longest chain 8 peptides. Score 0.446 Round 5: 71 peptides, 12 chains. Longest chain 12 peptides. Score 0.446 Taking the results from Round 3 Chains 12, Residues 60, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 1760 reflections ( 98.93 % complete ) and 2119 restraints for refining 998 atoms. 1843 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1918 (Rfree = 0.000) for 998 atoms. Found 5 (5 requested) and removed 6 (3 requested) atoms. Cycle 27: After refmac, R = 0.1778 (Rfree = 0.000) for 988 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 28: After refmac, R = 0.1626 (Rfree = 0.000) for 984 atoms. Found 0 (5 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.1582 (Rfree = 0.000) for 975 atoms. Found 2 (5 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1606 (Rfree = 0.000) for 973 atoms. Found 2 (5 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 4.15 Search for helices and strands: 0 residues in 0 chains, 1001 seeds are put forward Round 1: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.350 Round 2: 74 peptides, 11 chains. Longest chain 9 peptides. Score 0.520 Round 3: 63 peptides, 9 chains. Longest chain 11 peptides. Score 0.498 Round 4: 67 peptides, 9 chains. Longest chain 10 peptides. Score 0.538 Round 5: 69 peptides, 9 chains. Longest chain 17 peptides. Score 0.556 Taking the results from Round 5 Chains 9, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1760 reflections ( 98.93 % complete ) and 2297 restraints for refining 1029 atoms. 2066 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2251 (Rfree = 0.000) for 1029 atoms. Found 3 (5 requested) and removed 11 (3 requested) atoms. Cycle 32: After refmac, R = 0.1913 (Rfree = 0.000) for 1018 atoms. Found 2 (5 requested) and removed 3 (3 requested) atoms. Cycle 33: After refmac, R = 0.1875 (Rfree = 0.000) for 1015 atoms. Found 3 (5 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.1785 (Rfree = 0.000) for 1009 atoms. Found 2 (5 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.1871 (Rfree = 0.000) for 1007 atoms. Found 2 (5 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 4.11 Search for helices and strands: 0 residues in 0 chains, 1047 seeds are put forward Round 1: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.323 Round 2: 56 peptides, 9 chains. Longest chain 11 peptides. Score 0.424 Round 3: 59 peptides, 9 chains. Longest chain 12 peptides. Score 0.457 Round 4: 55 peptides, 9 chains. Longest chain 10 peptides. Score 0.412 Round 5: 61 peptides, 9 chains. Longest chain 11 peptides. Score 0.478 Taking the results from Round 5 Chains 9, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1760 reflections ( 98.93 % complete ) and 2330 restraints for refining 1013 atoms. 2131 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2227 (Rfree = 0.000) for 1013 atoms. Found 3 (5 requested) and removed 3 (3 requested) atoms. Cycle 37: After refmac, R = 0.2169 (Rfree = 0.000) for 1009 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.2077 (Rfree = 0.000) for 1007 atoms. Found 3 (5 requested) and removed 8 (3 requested) atoms. Cycle 39: After refmac, R = 0.1900 (Rfree = 0.000) for 996 atoms. Found 1 (5 requested) and removed 8 (3 requested) atoms. Cycle 40: After refmac, R = 0.2095 (Rfree = 0.000) for 985 atoms. Found 5 (5 requested) and removed 14 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 4.06 Search for helices and strands: 0 residues in 0 chains, 1005 seeds are put forward Round 1: 44 peptides, 9 chains. Longest chain 6 peptides. Score 0.278 Round 2: 39 peptides, 7 chains. Longest chain 7 peptides. Score 0.325 Round 3: 44 peptides, 8 chains. Longest chain 8 peptides. Score 0.333 Round 4: 48 peptides, 7 chains. Longest chain 12 peptides. Score 0.434 Round 5: 43 peptides, 7 chains. Longest chain 8 peptides. Score 0.375 Taking the results from Round 4 Chains 7, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1760 reflections ( 98.93 % complete ) and 2270 restraints for refining 981 atoms. 2113 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1979 (Rfree = 0.000) for 981 atoms. Found 3 (5 requested) and removed 5 (3 requested) atoms. Cycle 42: After refmac, R = 0.2230 (Rfree = 0.000) for 972 atoms. Found 4 (5 requested) and removed 8 (3 requested) atoms. Cycle 43: After refmac, R = 0.1762 (Rfree = 0.000) for 966 atoms. Found 0 (5 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.1713 (Rfree = 0.000) for 959 atoms. Found 2 (5 requested) and removed 6 (3 requested) atoms. Cycle 45: After refmac, R = 0.1471 (Rfree = 0.000) for 954 atoms. Found 1 (5 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 4.11 Search for helices and strands: 0 residues in 0 chains, 989 seeds are put forward Round 1: 39 peptides, 8 chains. Longest chain 10 peptides. Score 0.268 Round 2: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.299 Round 3: 54 peptides, 10 chains. Longest chain 9 peptides. Score 0.350 Round 4: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.416 Round 5: 63 peptides, 12 chains. Longest chain 10 peptides. Score 0.356 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 53, 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. 1760 reflections ( 98.93 % complete ) and 2136 restraints for refining 970 atoms. 1935 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2326 (Rfree = 0.000) for 970 atoms. Found 0 (5 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1798 (Rfree = 0.000) for 961 atoms. Found 0 (5 requested) and removed 2 (3 requested) atoms. Cycle 48: After refmac, R = 0.1708 (Rfree = 0.000) for 959 atoms. Found 0 (5 requested) and removed 2 (3 requested) atoms. Cycle 49: After refmac, R = 0.1673 (Rfree = 0.000) for 957 atoms. TimeTaking 24.47