Mon 24 Dec 00:05:08 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p10-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p10-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p10-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.8-parrot-mrncs ############### 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 00:05:12 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/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.8-parrot-mrncs/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 1464 and 0 Target number of residues in the AU: 1464 Target solvent content: 0.6585 Checking the provided sequence file Detected sequence length: 286 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1716 Adjusted target solvent content: 0.60 Input MTZ file: 2p10-3.8-parrot-mrncs.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: 146 Cell parameters: 180.269 180.269 185.514 90.000 90.000 120.000 Input sequence file: 2p10-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 13728 target number of atoms Had to go as low as 0.90 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: 119.449 3.800 Wilson plot Bfac: 83.94 21461 reflections ( 96.88 % complete ) and 0 restraints for refining 15238 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3147 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2789 (Rfree = 0.000) for 15238 atoms. Found 83 (83 requested) and removed 164 (41 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 3.22 Search for helices and strands: 0 residues in 0 chains, 15501 seeds are put forward NCS extension: 0 residues added, 15501 seeds are put forward Round 1: 751 peptides, 136 chains. Longest chain 16 peptides. Score 0.339 Round 2: 886 peptides, 120 chains. Longest chain 24 peptides. Score 0.483 Round 3: 952 peptides, 110 chains. Longest chain 30 peptides. Score 0.551 Round 4: 981 peptides, 112 chains. Longest chain 36 peptides. Score 0.562 Round 5: 989 peptides, 111 chains. Longest chain 34 peptides. Score 0.569 Taking the results from Round 5 Chains 127, Residues 878, Estimated correctness of the model 0.0 % 21 chains (210 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 27009 restraints for refining 12415 atoms. 22992 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2229 (Rfree = 0.000) for 12415 atoms. Found 65 (68 requested) and removed 131 (34 requested) atoms. Cycle 2: After refmac, R = 0.2116 (Rfree = 0.000) for 12135 atoms. Found 67 (67 requested) and removed 157 (33 requested) atoms. Cycle 3: After refmac, R = 0.1999 (Rfree = 0.000) for 11955 atoms. Found 66 (66 requested) and removed 117 (33 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1899 (Rfree = 0.000) for 11834 atoms. Found 60 (65 requested) and removed 70 (32 requested) atoms. Cycle 5: After refmac, R = 0.1821 (Rfree = 0.000) for 11775 atoms. Found 40 (65 requested) and removed 57 (32 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 3.16 Search for helices and strands: 0 residues in 0 chains, 12248 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 12269 seeds are put forward Round 1: 896 peptides, 133 chains. Longest chain 30 peptides. Score 0.451 Round 2: 967 peptides, 120 chains. Longest chain 25 peptides. Score 0.533 Round 3: 1002 peptides, 113 chains. Longest chain 33 peptides. Score 0.571 Round 4: 993 peptides, 121 chains. Longest chain 29 peptides. Score 0.545 Round 5: 975 peptides, 114 chains. Longest chain 27 peptides. Score 0.553 Taking the results from Round 3 Chains 130, Residues 889, Estimated correctness of the model 0.0 % 21 chains (205 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 26208 restraints for refining 12413 atoms. 22162 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2067 (Rfree = 0.000) for 12413 atoms. Found 68 (68 requested) and removed 254 (34 requested) atoms. Cycle 7: After refmac, R = 0.1911 (Rfree = 0.000) for 12101 atoms. Found 61 (67 requested) and removed 118 (33 requested) atoms. Cycle 8: After refmac, R = 0.1836 (Rfree = 0.000) for 11976 atoms. Found 54 (66 requested) and removed 90 (33 requested) atoms. Cycle 9: After refmac, R = 0.1779 (Rfree = 0.000) for 11879 atoms. Found 43 (65 requested) and removed 62 (32 requested) atoms. Cycle 10: After refmac, R = 0.1747 (Rfree = 0.000) for 11832 atoms. Found 31 (65 requested) and removed 70 (32 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.19 Search for helices and strands: 0 residues in 0 chains, 12274 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 12289 seeds are put forward Round 1: 901 peptides, 140 chains. Longest chain 21 peptides. Score 0.434 Round 2: 924 peptides, 121 chains. Longest chain 20 peptides. Score 0.504 Round 3: 954 peptides, 130 chains. Longest chain 20 peptides. Score 0.497 Round 4: 953 peptides, 122 chains. Longest chain 19 peptides. Score 0.519 Round 5: 967 peptides, 114 chains. Longest chain 24 peptides. Score 0.549 Taking the results from Round 5 Chains 125, Residues 853, Estimated correctness of the model 0.0 % 20 chains (171 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 27054 restraints for refining 12413 atoms. 23251 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2074 (Rfree = 0.000) for 12413 atoms. Found 68 (68 requested) and removed 131 (34 requested) atoms. Cycle 12: After refmac, R = 0.1938 (Rfree = 0.000) for 12234 atoms. Found 40 (67 requested) and removed 74 (33 requested) atoms. Cycle 13: After refmac, R = 0.1894 (Rfree = 0.000) for 12145 atoms. Found 42 (67 requested) and removed 71 (33 requested) atoms. Cycle 14: After refmac, R = 0.1839 (Rfree = 0.000) for 12088 atoms. Found 29 (66 requested) and removed 51 (33 requested) atoms. Cycle 15: After refmac, R = 0.1810 (Rfree = 0.000) for 12032 atoms. Found 37 (66 requested) and removed 60 (33 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.18 Search for helices and strands: 0 residues in 0 chains, 12493 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 12511 seeds are put forward Round 1: 830 peptides, 130 chains. Longest chain 16 peptides. Score 0.415 Round 2: 944 peptides, 126 chains. Longest chain 17 peptides. Score 0.502 Round 3: 972 peptides, 119 chains. Longest chain 24 peptides. Score 0.538 Round 4: 983 peptides, 123 chains. Longest chain 24 peptides. Score 0.534 Round 5: 979 peptides, 115 chains. Longest chain 32 peptides. Score 0.553 Taking the results from Round 5 Chains 123, Residues 864, Estimated correctness of the model 0.0 % 15 chains (123 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 27231 restraints for refining 12413 atoms. 23529 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2074 (Rfree = 0.000) for 12413 atoms. Found 64 (68 requested) and removed 73 (34 requested) atoms. Cycle 17: After refmac, R = 0.1998 (Rfree = 0.000) for 12328 atoms. Found 38 (68 requested) and removed 61 (34 requested) atoms. Cycle 18: After refmac, R = 0.1971 (Rfree = 0.000) for 12268 atoms. Found 46 (67 requested) and removed 62 (33 requested) atoms. Cycle 19: After refmac, R = 0.1891 (Rfree = 0.000) for 12230 atoms. Found 42 (67 requested) and removed 56 (33 requested) atoms. Cycle 20: After refmac, R = 0.1828 (Rfree = 0.000) for 12183 atoms. Found 38 (67 requested) and removed 58 (33 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.18 Search for helices and strands: 0 residues in 0 chains, 12623 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 12642 seeds are put forward Round 1: 821 peptides, 137 chains. Longest chain 15 peptides. Score 0.387 Round 2: 885 peptides, 121 chains. Longest chain 23 peptides. Score 0.479 Round 3: 890 peptides, 114 chains. Longest chain 27 peptides. Score 0.503 Round 4: 902 peptides, 121 chains. Longest chain 27 peptides. Score 0.490 Round 5: 936 peptides, 119 chains. Longest chain 27 peptides. Score 0.517 Taking the results from Round 5 Chains 125, Residues 817, Estimated correctness of the model 0.0 % 14 chains (104 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 28020 restraints for refining 12417 atoms. 24591 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2100 (Rfree = 0.000) for 12417 atoms. Found 59 (68 requested) and removed 59 (34 requested) atoms. Cycle 22: After refmac, R = 0.1908 (Rfree = 0.000) for 12335 atoms. Found 33 (68 requested) and removed 64 (34 requested) atoms. Cycle 23: After refmac, R = 0.1910 (Rfree = 0.000) for 12252 atoms. Found 67 (67 requested) and removed 138 (33 requested) atoms. Cycle 24: After refmac, R = 0.1849 (Rfree = 0.000) for 12157 atoms. Found 28 (66 requested) and removed 82 (33 requested) atoms. Cycle 25: After refmac, R = 0.1832 (Rfree = 0.000) for 12072 atoms. Found 21 (66 requested) and removed 63 (33 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.17 Search for helices and strands: 0 residues in 0 chains, 12435 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 12460 seeds are put forward Round 1: 749 peptides, 130 chains. Longest chain 15 peptides. Score 0.357 Round 2: 843 peptides, 126 chains. Longest chain 17 peptides. Score 0.436 Round 3: 854 peptides, 125 chains. Longest chain 18 peptides. Score 0.447 Round 4: 887 peptides, 128 chains. Longest chain 18 peptides. Score 0.460 Round 5: 894 peptides, 121 chains. Longest chain 19 peptides. Score 0.485 Taking the results from Round 5 Chains 131, Residues 773, Estimated correctness of the model 0.0 % 29 chains (214 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 21461 reflections ( 96.88 % complete ) and 26978 restraints for refining 12416 atoms. 23391 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2142 (Rfree = 0.000) for 12416 atoms. Found 61 (68 requested) and removed 88 (34 requested) atoms. Cycle 27: After refmac, R = 0.2000 (Rfree = 0.000) for 12273 atoms. Found 51 (68 requested) and removed 76 (34 requested) atoms. Cycle 28: After refmac, R = 0.1931 (Rfree = 0.000) for 12203 atoms. Found 52 (67 requested) and removed 57 (33 requested) atoms. Cycle 29: After refmac, R = 0.1917 (Rfree = 0.000) for 12159 atoms. Found 54 (67 requested) and removed 67 (33 requested) atoms. Cycle 30: After refmac, R = 0.1867 (Rfree = 0.000) for 12120 atoms. Found 45 (66 requested) and removed 43 (33 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.17 Search for helices and strands: 0 residues in 0 chains, 12564 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 12580 seeds are put forward Round 1: 773 peptides, 138 chains. Longest chain 18 peptides. Score 0.349 Round 2: 868 peptides, 131 chains. Longest chain 22 peptides. Score 0.438 Round 3: 901 peptides, 127 chains. Longest chain 27 peptides. Score 0.472 Round 4: 908 peptides, 128 chains. Longest chain 21 peptides. Score 0.474 Round 5: 882 peptides, 120 chains. Longest chain 19 peptides. Score 0.480 Taking the results from Round 5 Chains 121, Residues 762, Estimated correctness of the model 0.0 % 8 chains (59 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 28496 restraints for refining 12412 atoms. 25413 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2140 (Rfree = 0.000) for 12412 atoms. Found 58 (68 requested) and removed 58 (34 requested) atoms. Cycle 32: After refmac, R = 0.1923 (Rfree = 0.000) for 12351 atoms. Found 59 (68 requested) and removed 189 (34 requested) atoms. Cycle 33: After refmac, R = 0.1908 (Rfree = 0.000) for 12198 atoms. Found 43 (67 requested) and removed 100 (33 requested) atoms. Cycle 34: After refmac, R = 0.1872 (Rfree = 0.000) for 12118 atoms. Found 54 (66 requested) and removed 52 (33 requested) atoms. Cycle 35: After refmac, R = 0.1887 (Rfree = 0.000) for 12095 atoms. Found 66 (66 requested) and removed 61 (33 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 3.16 Search for helices and strands: 0 residues in 0 chains, 12528 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 12550 seeds are put forward Round 1: 754 peptides, 144 chains. Longest chain 13 peptides. Score 0.315 Round 2: 806 peptides, 122 chains. Longest chain 21 peptides. Score 0.423 Round 3: 822 peptides, 122 chains. Longest chain 17 peptides. Score 0.434 Round 4: 821 peptides, 117 chains. Longest chain 30 peptides. Score 0.449 Round 5: 820 peptides, 116 chains. Longest chain 26 peptides. Score 0.451 Taking the results from Round 5 Chains 120, Residues 704, Estimated correctness of the model 0.0 % 14 chains (108 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 21461 reflections ( 96.88 % complete ) and 28495 restraints for refining 12413 atoms. 25500 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2074 (Rfree = 0.000) for 12413 atoms. Found 68 (68 requested) and removed 116 (34 requested) atoms. Cycle 37: After refmac, R = 0.1931 (Rfree = 0.000) for 12291 atoms. Found 54 (67 requested) and removed 106 (33 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1909 (Rfree = 0.000) for 12206 atoms. Found 60 (67 requested) and removed 81 (33 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1846 (Rfree = 0.000) for 12151 atoms. Found 65 (67 requested) and removed 87 (33 requested) atoms. Cycle 40: After refmac, R = 0.1785 (Rfree = 0.000) for 12111 atoms. Found 40 (66 requested) and removed 66 (33 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.17 Search for helices and strands: 0 residues in 0 chains, 12543 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 12575 seeds are put forward Round 1: 668 peptides, 126 chains. Longest chain 14 peptides. Score 0.308 Round 2: 769 peptides, 118 chains. Longest chain 26 peptides. Score 0.410 Round 3: 783 peptides, 118 chains. Longest chain 26 peptides. Score 0.420 Round 4: 801 peptides, 123 chains. Longest chain 21 peptides. Score 0.417 Round 5: 782 peptides, 117 chains. Longest chain 26 peptides. Score 0.422 Taking the results from Round 5 Chains 122, Residues 665, Estimated correctness of the model 0.0 % 21 chains (136 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 28189 restraints for refining 12416 atoms. 25312 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2013 (Rfree = 0.000) for 12416 atoms. Found 68 (68 requested) and removed 83 (34 requested) atoms. Cycle 42: After refmac, R = 0.1914 (Rfree = 0.000) for 12343 atoms. Found 68 (68 requested) and removed 70 (34 requested) atoms. Cycle 43: After refmac, R = 0.1892 (Rfree = 0.000) for 12312 atoms. Found 67 (67 requested) and removed 65 (33 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1797 (Rfree = 0.000) for 12302 atoms. Found 62 (67 requested) and removed 57 (33 requested) atoms. Cycle 45: After refmac, R = 0.1804 (Rfree = 0.000) for 12293 atoms. Found 64 (67 requested) and removed 60 (33 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 3.15 Search for helices and strands: 0 residues in 0 chains, 12778 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 12799 seeds are put forward Round 1: 665 peptides, 133 chains. Longest chain 11 peptides. Score 0.282 Round 2: 740 peptides, 124 chains. Longest chain 20 peptides. Score 0.370 Round 3: 742 peptides, 118 chains. Longest chain 19 peptides. Score 0.391 Round 4: 753 peptides, 111 chains. Longest chain 20 peptides. Score 0.421 Round 5: 791 peptides, 121 chains. Longest chain 18 peptides. Score 0.416 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 116, Residues 642, Estimated correctness of the model 0.0 % 7 chains (69 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2p10-3_warpNtrace.pdb as input Building loops using Loopy2018 116 chains (642 residues) following loop building 7 chains (69 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 21461 reflections ( 96.88 % complete ) and 29053 restraints for refining 12413 atoms. 26400 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1927 (Rfree = 0.000) for 12413 atoms. Found 0 (68 requested) and removed 34 (34 requested) atoms. Cycle 47: After refmac, R = 0.1881 (Rfree = 0.000) for 12332 atoms. Found 0 (68 requested) and removed 34 (34 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1847 (Rfree = 0.000) for 12264 atoms. Found 0 (67 requested) and removed 33 (33 requested) atoms. Cycle 49: After refmac, R = 0.1772 (Rfree = 0.000) for 12202 atoms. TimeTaking 143.03