Mon 24 Dec 07:26:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2i8d-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i8d-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i8d-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-4.0-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:27:00 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/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-4.0-parrot-noncs/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 194 and 0 Target number of residues in the AU: 194 Target solvent content: 0.6529 Checking the provided sequence file Detected sequence length: 123 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 246 Adjusted target solvent content: 0.56 Input MTZ file: 2i8d-4.0-parrot-noncs.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: 19 Cell parameters: 47.981 69.366 90.889 90.000 90.000 90.000 Input sequence file: 2i8d-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 1968 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 55.142 4.000 Wilson plot Bfac: 79.92 2744 reflections ( 98.21 % complete ) and 0 restraints for refining 2169 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3557 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3494 (Rfree = 0.000) for 2169 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.42 Search for helices and strands: 0 residues in 0 chains, 2215 seeds are put forward NCS extension: 0 residues added, 2215 seeds are put forward Round 1: 119 peptides, 25 chains. Longest chain 9 peptides. Score 0.283 Round 2: 147 peptides, 21 chains. Longest chain 19 peptides. Score 0.518 Round 3: 152 peptides, 20 chains. Longest chain 18 peptides. Score 0.560 Round 4: 142 peptides, 18 chains. Longest chain 18 peptides. Score 0.556 Round 5: 147 peptides, 18 chains. Longest chain 25 peptides. Score 0.577 Taking the results from Round 5 Chains 18, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3999 restraints for refining 1773 atoms. 3501 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3358 (Rfree = 0.000) for 1773 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 2: After refmac, R = 0.2946 (Rfree = 0.000) for 1738 atoms. Found 7 (8 requested) and removed 13 (4 requested) atoms. Cycle 3: After refmac, R = 0.2880 (Rfree = 0.000) for 1710 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 4: After refmac, R = 0.2430 (Rfree = 0.000) for 1695 atoms. Found 5 (8 requested) and removed 10 (4 requested) atoms. Cycle 5: After refmac, R = 0.2705 (Rfree = 0.000) for 1681 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.43 Search for helices and strands: 0 residues in 0 chains, 1745 seeds are put forward NCS extension: 40 residues added (3 deleted due to clashes), 1785 seeds are put forward Round 1: 113 peptides, 16 chains. Longest chain 17 peptides. Score 0.462 Round 2: 128 peptides, 18 chains. Longest chain 14 peptides. Score 0.492 Round 3: 135 peptides, 16 chains. Longest chain 13 peptides. Score 0.565 Round 4: 129 peptides, 17 chains. Longest chain 14 peptides. Score 0.518 Round 5: 128 peptides, 15 chains. Longest chain 20 peptides. Score 0.555 Taking the results from Round 3 Chains 16, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3966 restraints for refining 1776 atoms. 3506 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3255 (Rfree = 0.000) for 1776 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 7: After refmac, R = 0.2842 (Rfree = 0.000) for 1750 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 8: After refmac, R = 0.2164 (Rfree = 0.000) for 1723 atoms. Found 4 (8 requested) and removed 10 (4 requested) atoms. Cycle 9: After refmac, R = 0.2416 (Rfree = 0.000) for 1711 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 10: After refmac, R = 0.2569 (Rfree = 0.000) for 1693 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 3.34 Search for helices and strands: 0 residues in 0 chains, 1753 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1768 seeds are put forward Round 1: 116 peptides, 21 chains. Longest chain 9 peptides. Score 0.362 Round 2: 130 peptides, 17 chains. Longest chain 17 peptides. Score 0.523 Round 3: 136 peptides, 18 chains. Longest chain 14 peptides. Score 0.529 Round 4: 140 peptides, 17 chains. Longest chain 23 peptides. Score 0.567 Round 5: 136 peptides, 16 chains. Longest chain 13 peptides. Score 0.570 Taking the results from Round 5 Chains 16, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 4000 restraints for refining 1777 atoms. 3536 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2763 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 12: After refmac, R = 0.2692 (Rfree = 0.000) for 1754 atoms. Found 8 (8 requested) and removed 22 (4 requested) atoms. Cycle 13: After refmac, R = 0.2647 (Rfree = 0.000) for 1731 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 14: After refmac, R = 0.2867 (Rfree = 0.000) for 1721 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 15: After refmac, R = 0.2471 (Rfree = 0.000) for 1710 atoms. Found 1 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.41 Search for helices and strands: 0 residues in 0 chains, 1770 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1787 seeds are put forward Round 1: 106 peptides, 17 chains. Longest chain 11 peptides. Score 0.402 Round 2: 115 peptides, 14 chains. Longest chain 17 peptides. Score 0.517 Round 3: 120 peptides, 15 chains. Longest chain 15 peptides. Score 0.519 Round 4: 126 peptides, 15 chains. Longest chain 13 peptides. Score 0.546 Round 5: 118 peptides, 17 chains. Longest chain 12 peptides. Score 0.465 Taking the results from Round 4 Chains 15, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 4065 restraints for refining 1776 atoms. 3636 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3248 (Rfree = 0.000) for 1776 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 17: After refmac, R = 0.2848 (Rfree = 0.000) for 1760 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 18: After refmac, R = 0.2141 (Rfree = 0.000) for 1744 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2550 (Rfree = 0.000) for 1737 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 20: After refmac, R = 0.2173 (Rfree = 0.000) for 1724 atoms. Found 4 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.70 3.41 Search for helices and strands: 0 residues in 0 chains, 1772 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 1785 seeds are put forward Round 1: 100 peptides, 19 chains. Longest chain 10 peptides. Score 0.319 Round 2: 114 peptides, 15 chains. Longest chain 12 peptides. Score 0.490 Round 3: 109 peptides, 17 chains. Longest chain 12 peptides. Score 0.419 Round 4: 107 peptides, 18 chains. Longest chain 13 peptides. Score 0.384 Round 5: 111 peptides, 16 chains. Longest chain 15 peptides. Score 0.452 Taking the results from Round 2 Chains 15, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3902 restraints for refining 1770 atoms. 3521 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2750 (Rfree = 0.000) for 1770 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 22: After refmac, R = 0.2672 (Rfree = 0.000) for 1747 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 23: After refmac, R = 0.2633 (Rfree = 0.000) for 1726 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 24: After refmac, R = 0.2324 (Rfree = 0.000) for 1712 atoms. Found 5 (8 requested) and removed 11 (4 requested) atoms. Cycle 25: After refmac, R = 0.2392 (Rfree = 0.000) for 1702 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.30 Search for helices and strands: 0 residues in 0 chains, 1738 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 1752 seeds are put forward Round 1: 109 peptides, 20 chains. Longest chain 12 peptides. Score 0.347 Round 2: 115 peptides, 17 chains. Longest chain 13 peptides. Score 0.450 Round 3: 112 peptides, 15 chains. Longest chain 15 peptides. Score 0.480 Round 4: 112 peptides, 16 chains. Longest chain 13 peptides. Score 0.457 Round 5: 108 peptides, 15 chains. Longest chain 17 peptides. Score 0.460 Taking the results from Round 3 Chains 15, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3951 restraints for refining 1777 atoms. 3578 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2636 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 27: After refmac, R = 0.2204 (Rfree = 0.000) for 1767 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 28: After refmac, R = 0.2574 (Rfree = 0.000) for 1757 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 29: After refmac, R = 0.1825 (Rfree = 0.000) for 1742 atoms. Found 0 (8 requested) and removed 11 (4 requested) atoms. Cycle 30: After refmac, R = 0.1736 (Rfree = 0.000) for 1730 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.45 Search for helices and strands: 0 residues in 0 chains, 1770 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1787 seeds are put forward Round 1: 102 peptides, 21 chains. Longest chain 9 peptides. Score 0.281 Round 2: 116 peptides, 20 chains. Longest chain 10 peptides. Score 0.386 Round 3: 113 peptides, 18 chains. Longest chain 12 peptides. Score 0.416 Round 4: 101 peptides, 15 chains. Longest chain 16 peptides. Score 0.424 Round 5: 105 peptides, 16 chains. Longest chain 11 peptides. Score 0.421 Taking the results from Round 4 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 4089 restraints for refining 1777 atoms. 3760 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2609 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 32: After refmac, R = 0.2195 (Rfree = 0.000) for 1761 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 33: After refmac, R = 0.2454 (Rfree = 0.000) for 1748 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 34: After refmac, R = 0.2068 (Rfree = 0.000) for 1738 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. Cycle 35: After refmac, R = 0.2289 (Rfree = 0.000) for 1730 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.42 Search for helices and strands: 0 residues in 0 chains, 1765 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1786 seeds are put forward Round 1: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.288 Round 2: 89 peptides, 15 chains. Longest chain 10 peptides. Score 0.357 Round 3: 95 peptides, 13 chains. Longest chain 16 peptides. Score 0.440 Round 4: 101 peptides, 17 chains. Longest chain 15 peptides. Score 0.375 Round 5: 106 peptides, 18 chains. Longest chain 12 peptides. Score 0.378 Taking the results from Round 3 Chains 14, Residues 82, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3994 restraints for refining 1777 atoms. 3632 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2649 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 37: After refmac, R = 0.2305 (Rfree = 0.000) for 1769 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 38: After refmac, R = 0.2257 (Rfree = 0.000) for 1758 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 39: After refmac, R = 0.2202 (Rfree = 0.000) for 1747 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.2545 (Rfree = 0.000) for 1742 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.41 Search for helices and strands: 0 residues in 0 chains, 1788 seeds are put forward NCS extension: 0 residues added, 1788 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 10 peptides. Score 0.294 Round 2: 85 peptides, 15 chains. Longest chain 12 peptides. Score 0.333 Round 3: 85 peptides, 13 chains. Longest chain 12 peptides. Score 0.385 Round 4: 86 peptides, 15 chains. Longest chain 9 peptides. Score 0.339 Round 5: 98 peptides, 15 chains. Longest chain 10 peptides. Score 0.407 Taking the results from Round 5 Chains 15, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 4108 restraints for refining 1777 atoms. 3791 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2887 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 42: After refmac, R = 0.2127 (Rfree = 0.000) for 1762 atoms. Found 8 (8 requested) and removed 25 (4 requested) atoms. Cycle 43: After refmac, R = 0.2413 (Rfree = 0.000) for 1739 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 44: After refmac, R = 0.2272 (Rfree = 0.000) for 1735 atoms. Found 8 (8 requested) and removed 59 (4 requested) atoms. Cycle 45: After refmac, R = 0.2193 (Rfree = 0.000) for 1679 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.36 Search for helices and strands: 0 residues in 0 chains, 1716 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 1728 seeds are put forward Round 1: 70 peptides, 16 chains. Longest chain 7 peptides. Score 0.209 Round 2: 81 peptides, 16 chains. Longest chain 7 peptides. Score 0.282 Round 3: 88 peptides, 17 chains. Longest chain 10 peptides. Score 0.299 Round 4: 85 peptides, 16 chains. Longest chain 8 peptides. Score 0.307 Round 5: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.337 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 74, 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 2i8d-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2744 reflections ( 98.21 % complete ) and 3947 restraints for refining 1720 atoms. 3667 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2570 (Rfree = 0.000) for 1720 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2157 (Rfree = 0.000) for 1713 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2473 (Rfree = 0.000) for 1701 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2241 (Rfree = 0.000) for 1694 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... TimeTaking 25.1