Sun 23 Dec 22:22:52 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 2ess-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ess-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ess-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-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/2ess-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-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 22:23:00 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/2ess-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-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 195 and 0 Target number of residues in the AU: 195 Target solvent content: 0.6603 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 248 Adjusted target solvent content: 0.57 Input MTZ file: 2ess-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: 152 Cell parameters: 91.150 91.150 64.770 90.000 90.000 120.000 Input sequence file: 2ess-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.85 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: 29.962 3.600 Wilson plot Bfac: 84.29 3775 reflections ( 99.76 % complete ) and 0 restraints for refining 2208 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3681 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3568 (Rfree = 0.000) for 2208 atoms. Found 12 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.24 Search for helices and strands: 0 residues in 0 chains, 2225 seeds are put forward Round 1: 93 peptides, 18 chains. Longest chain 10 peptides. Score 0.300 Round 2: 110 peptides, 18 chains. Longest chain 12 peptides. Score 0.396 Round 3: 114 peptides, 20 chains. Longest chain 11 peptides. Score 0.370 Round 4: 122 peptides, 19 chains. Longest chain 12 peptides. Score 0.435 Round 5: 121 peptides, 16 chains. Longest chain 13 peptides. Score 0.495 Taking the results from Round 5 Chains 16, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3775 reflections ( 99.76 % complete ) and 4108 restraints for refining 1799 atoms. 3704 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3431 (Rfree = 0.000) for 1799 atoms. Found 11 (11 requested) and removed 32 (5 requested) atoms. Cycle 2: After refmac, R = 0.3005 (Rfree = 0.000) for 1745 atoms. Found 10 (11 requested) and removed 16 (5 requested) atoms. Cycle 3: After refmac, R = 0.2991 (Rfree = 0.000) for 1721 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 4: After refmac, R = 0.2866 (Rfree = 0.000) for 1709 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 5: After refmac, R = 0.3014 (Rfree = 0.000) for 1695 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 1739 seeds are put forward Round 1: 116 peptides, 24 chains. Longest chain 12 peptides. Score 0.287 Round 2: 126 peptides, 20 chains. Longest chain 13 peptides. Score 0.433 Round 3: 117 peptides, 17 chains. Longest chain 14 peptides. Score 0.454 Round 4: 114 peptides, 18 chains. Longest chain 14 peptides. Score 0.417 Round 5: 112 peptides, 15 chains. Longest chain 13 peptides. Score 0.474 Taking the results from Round 5 Chains 15, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3775 reflections ( 99.76 % complete ) and 4112 restraints for refining 1750 atoms. 3739 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2696 (Rfree = 0.000) for 1750 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 7: After refmac, R = 0.2685 (Rfree = 0.000) for 1722 atoms. Found 6 (11 requested) and removed 11 (5 requested) atoms. Cycle 8: After refmac, R = 0.2586 (Rfree = 0.000) for 1711 atoms. Found 4 (11 requested) and removed 11 (5 requested) atoms. Cycle 9: After refmac, R = 0.2266 (Rfree = 0.000) for 1698 atoms. Found 0 (10 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2359 (Rfree = 0.000) for 1687 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 1732 seeds are put forward Round 1: 121 peptides, 20 chains. Longest chain 14 peptides. Score 0.407 Round 2: 134 peptides, 23 chains. Longest chain 14 peptides. Score 0.407 Round 3: 131 peptides, 18 chains. Longest chain 17 peptides. Score 0.500 Round 4: 126 peptides, 18 chains. Longest chain 14 peptides. Score 0.476 Round 5: 139 peptides, 19 chains. Longest chain 20 peptides. Score 0.516 Taking the results from Round 5 Chains 19, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3775 reflections ( 99.76 % complete ) and 4032 restraints for refining 1794 atoms. 3571 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2538 (Rfree = 0.000) for 1794 atoms. Found 4 (11 requested) and removed 14 (5 requested) atoms. Cycle 12: After refmac, R = 0.2605 (Rfree = 0.000) for 1772 atoms. Found 8 (11 requested) and removed 14 (5 requested) atoms. Cycle 13: After refmac, R = 0.2492 (Rfree = 0.000) for 1762 atoms. Found 6 (11 requested) and removed 13 (5 requested) atoms. Cycle 14: After refmac, R = 0.2273 (Rfree = 0.000) for 1755 atoms. Found 0 (11 requested) and removed 9 (5 requested) atoms. Cycle 15: After refmac, R = 0.2412 (Rfree = 0.000) for 1743 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 1814 seeds are put forward Round 1: 99 peptides, 18 chains. Longest chain 9 peptides. Score 0.335 Round 2: 115 peptides, 15 chains. Longest chain 17 peptides. Score 0.488 Round 3: 113 peptides, 18 chains. Longest chain 14 peptides. Score 0.411 Round 4: 116 peptides, 19 chains. Longest chain 13 peptides. Score 0.404 Round 5: 116 peptides, 18 chains. Longest chain 11 peptides. Score 0.427 Taking the results from Round 2 Chains 15, Residues 100, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3775 reflections ( 99.76 % complete ) and 4080 restraints for refining 1799 atoms. 3666 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2659 (Rfree = 0.000) for 1799 atoms. Found 4 (11 requested) and removed 15 (5 requested) atoms. Cycle 17: After refmac, R = 0.2909 (Rfree = 0.000) for 1779 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 18: After refmac, R = 0.2563 (Rfree = 0.000) for 1766 atoms. Found 4 (11 requested) and removed 11 (5 requested) atoms. Cycle 19: After refmac, R = 0.2288 (Rfree = 0.000) for 1752 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.2252 (Rfree = 0.000) for 1742 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 1786 seeds are put forward Round 1: 91 peptides, 21 chains. Longest chain 6 peptides. Score 0.212 Round 2: 107 peptides, 18 chains. Longest chain 12 peptides. Score 0.380 Round 3: 113 peptides, 21 chains. Longest chain 11 peptides. Score 0.341 Round 4: 112 peptides, 21 chains. Longest chain 11 peptides. Score 0.336 Round 5: 124 peptides, 21 chains. Longest chain 11 peptides. Score 0.400 Taking the results from Round 5 Chains 22, Residues 103, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3775 reflections ( 99.76 % complete ) and 4036 restraints for refining 1799 atoms. 3613 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2721 (Rfree = 0.000) for 1799 atoms. Found 3 (11 requested) and removed 12 (5 requested) atoms. Cycle 22: After refmac, R = 0.2481 (Rfree = 0.000) for 1778 atoms. Found 4 (11 requested) and removed 11 (5 requested) atoms. Cycle 23: After refmac, R = 0.2378 (Rfree = 0.000) for 1762 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. Cycle 24: After refmac, R = 0.2344 (Rfree = 0.000) for 1754 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 25: After refmac, R = 0.2267 (Rfree = 0.000) for 1747 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 1800 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 12 peptides. Score 0.295 Round 2: 102 peptides, 18 chains. Longest chain 12 peptides. Score 0.352 Round 3: 112 peptides, 19 chains. Longest chain 13 peptides. Score 0.383 Round 4: 102 peptides, 19 chains. Longest chain 13 peptides. Score 0.328 Round 5: 109 peptides, 17 chains. Longest chain 14 peptides. Score 0.414 Taking the results from Round 5 Chains 17, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3775 reflections ( 99.76 % complete ) and 4243 restraints for refining 1799 atoms. 3892 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2615 (Rfree = 0.000) for 1799 atoms. Found 8 (11 requested) and removed 11 (5 requested) atoms. Cycle 27: After refmac, R = 0.2525 (Rfree = 0.000) for 1786 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.2195 (Rfree = 0.000) for 1777 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.2287 (Rfree = 0.000) for 1769 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.2103 (Rfree = 0.000) for 1764 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 1800 seeds are put forward Round 1: 81 peptides, 18 chains. Longest chain 7 peptides. Score 0.227 Round 2: 103 peptides, 18 chains. Longest chain 16 peptides. Score 0.358 Round 3: 113 peptides, 19 chains. Longest chain 11 peptides. Score 0.388 Round 4: 108 peptides, 20 chains. Longest chain 14 peptides. Score 0.337 Round 5: 105 peptides, 17 chains. Longest chain 14 peptides. Score 0.392 Taking the results from Round 5 Chains 17, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3775 reflections ( 99.76 % complete ) and 4153 restraints for refining 1799 atoms. 3818 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2373 (Rfree = 0.000) for 1799 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 32: After refmac, R = 0.2440 (Rfree = 0.000) for 1787 atoms. Found 9 (11 requested) and removed 8 (5 requested) atoms. Cycle 33: After refmac, R = 0.2463 (Rfree = 0.000) for 1782 atoms. Found 8 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2480 (Rfree = 0.000) for 1783 atoms. Found 10 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2417 (Rfree = 0.000) for 1779 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.24 Search for helices and strands: 0 residues in 0 chains, 1823 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 10 peptides. Score 0.253 Round 2: 76 peptides, 12 chains. Longest chain 14 peptides. Score 0.356 Round 3: 79 peptides, 13 chains. Longest chain 13 peptides. Score 0.347 Round 4: 86 peptides, 14 chains. Longest chain 12 peptides. Score 0.361 Round 5: 86 peptides, 14 chains. Longest chain 13 peptides. Score 0.361 Taking the results from Round 5 Chains 15, Residues 72, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3775 reflections ( 99.76 % complete ) and 4100 restraints for refining 1799 atoms. 3767 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2492 (Rfree = 0.000) for 1799 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 37: After refmac, R = 0.2656 (Rfree = 0.000) for 1795 atoms. Found 10 (11 requested) and removed 6 (5 requested) atoms. Cycle 38: After refmac, R = 0.2501 (Rfree = 0.000) for 1792 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.2490 (Rfree = 0.000) for 1787 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.2400 (Rfree = 0.000) for 1785 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 1826 seeds are put forward Round 1: 93 peptides, 20 chains. Longest chain 9 peptides. Score 0.250 Round 2: 104 peptides, 20 chains. Longest chain 8 peptides. Score 0.315 Round 3: 95 peptides, 18 chains. Longest chain 10 peptides. Score 0.312 Round 4: 96 peptides, 18 chains. Longest chain 12 peptides. Score 0.318 Round 5: 88 peptides, 17 chains. Longest chain 12 peptides. Score 0.296 Taking the results from Round 4 Chains 18, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3775 reflections ( 99.76 % complete ) and 4239 restraints for refining 1799 atoms. 3945 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2408 (Rfree = 0.000) for 1799 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 42: After refmac, R = 0.2349 (Rfree = 0.000) for 1786 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 43: After refmac, R = 0.2346 (Rfree = 0.000) for 1777 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2060 (Rfree = 0.000) for 1776 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2373 (Rfree = 0.000) for 1768 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 1803 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 6 peptides. Score 0.221 Round 2: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.269 Round 3: 76 peptides, 15 chains. Longest chain 8 peptides. Score 0.275 Round 4: 78 peptides, 15 chains. Longest chain 8 peptides. Score 0.288 Round 5: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.296 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 71, 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 2ess-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3775 reflections ( 99.76 % complete ) and 4201 restraints for refining 1799 atoms. 3934 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2406 (Rfree = 0.000) for 1799 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2512 (Rfree = 0.000) for 1788 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2404 (Rfree = 0.000) for 1773 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2397 (Rfree = 0.000) for 1764 atoms. TimeTaking 33.02