Sun 23 Dec 22:23:02 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 2p10-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p10-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p10-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-3.8-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/2p10-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-3.8-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 22:23:11 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/2p10-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-3.8-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 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-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: 146 Cell parameters: 180.269 180.269 185.514 90.000 90.000 120.000 Input sequence file: 2p10-3.8-parrot-hancs.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 15191 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3121 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2762 (Rfree = 0.000) for 15191 atoms. Found 83 (83 requested) and removed 159 (41 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.20 Search for helices and strands: 0 residues in 0 chains, 15447 seeds are put forward NCS extension: 0 residues added, 15447 seeds are put forward Round 1: 767 peptides, 137 chains. Longest chain 20 peptides. Score 0.348 Round 2: 939 peptides, 125 chains. Longest chain 20 peptides. Score 0.502 Round 3: 947 peptides, 115 chains. Longest chain 23 peptides. Score 0.534 Round 4: 965 peptides, 108 chains. Longest chain 35 peptides. Score 0.564 Round 5: 973 peptides, 106 chains. Longest chain 35 peptides. Score 0.573 Taking the results from Round 5 Chains 113, Residues 867, Estimated correctness of the model 0.0 % 17 chains (169 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 27250 restraints for refining 12414 atoms. 23412 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2183 (Rfree = 0.000) for 12414 atoms. Found 68 (68 requested) and removed 143 (34 requested) atoms. Cycle 2: After refmac, R = 0.2024 (Rfree = 0.000) for 12157 atoms. Found 67 (67 requested) and removed 80 (33 requested) atoms. Cycle 3: After refmac, R = 0.1975 (Rfree = 0.000) for 12082 atoms. Found 52 (66 requested) and removed 84 (33 requested) atoms. Cycle 4: After refmac, R = 0.1922 (Rfree = 0.000) for 12007 atoms. Found 39 (66 requested) and removed 127 (33 requested) atoms. Cycle 5: After refmac, R = 0.1887 (Rfree = 0.000) for 11876 atoms. Found 43 (65 requested) and removed 95 (32 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.19 Search for helices and strands: 0 residues in 0 chains, 12362 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 12377 seeds are put forward Round 1: 891 peptides, 137 chains. Longest chain 20 peptides. Score 0.436 Round 2: 953 peptides, 117 chains. Longest chain 23 peptides. Score 0.532 Round 3: 981 peptides, 113 chains. Longest chain 32 peptides. Score 0.559 Round 4: 1008 peptides, 109 chains. Longest chain 42 peptides. Score 0.585 Round 5: 1010 peptides, 108 chains. Longest chain 28 peptides. Score 0.589 Taking the results from Round 5 Chains 121, Residues 902, Estimated correctness of the model 0.0 % 25 chains (237 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 26238 restraints for refining 12415 atoms. 22082 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2101 (Rfree = 0.000) for 12415 atoms. Found 68 (68 requested) and removed 206 (34 requested) atoms. Cycle 7: After refmac, R = 0.1957 (Rfree = 0.000) for 12165 atoms. Found 50 (67 requested) and removed 125 (33 requested) atoms. Cycle 8: After refmac, R = 0.1921 (Rfree = 0.000) for 12033 atoms. Found 50 (66 requested) and removed 93 (33 requested) atoms. Cycle 9: After refmac, R = 0.1863 (Rfree = 0.000) for 11941 atoms. Found 49 (65 requested) and removed 90 (32 requested) atoms. Cycle 10: After refmac, R = 0.1825 (Rfree = 0.000) for 11854 atoms. Found 60 (65 requested) and removed 71 (32 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.19 Search for helices and strands: 0 residues in 0 chains, 12255 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 12277 seeds are put forward Round 1: 877 peptides, 134 chains. Longest chain 25 peptides. Score 0.435 Round 2: 965 peptides, 123 chains. Longest chain 38 peptides. Score 0.523 Round 3: 949 peptides, 117 chains. Longest chain 24 peptides. Score 0.530 Round 4: 933 peptides, 108 chains. Longest chain 28 peptides. Score 0.545 Round 5: 969 peptides, 116 chains. Longest chain 32 peptides. Score 0.545 Taking the results from Round 5 Chains 138, Residues 853, Estimated correctness of the model 0.0 % 29 chains (231 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 21461 reflections ( 96.88 % complete ) and 26321 restraints for refining 12414 atoms. 22448 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2152 (Rfree = 0.000) for 12414 atoms. Found 68 (68 requested) and removed 146 (34 requested) atoms. Cycle 12: After refmac, R = 0.1968 (Rfree = 0.000) for 12227 atoms. Found 45 (67 requested) and removed 91 (33 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1881 (Rfree = 0.000) for 12132 atoms. Found 33 (66 requested) and removed 76 (33 requested) atoms. Cycle 14: After refmac, R = 0.1812 (Rfree = 0.000) for 12056 atoms. Found 24 (66 requested) and removed 72 (33 requested) atoms. Cycle 15: After refmac, R = 0.1775 (Rfree = 0.000) for 11984 atoms. Found 24 (66 requested) and removed 53 (33 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.17 Search for helices and strands: 0 residues in 0 chains, 12444 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 12465 seeds are put forward Round 1: 817 peptides, 127 chains. Longest chain 26 peptides. Score 0.416 Round 2: 899 peptides, 115 chains. Longest chain 24 peptides. Score 0.505 Round 3: 912 peptides, 113 chains. Longest chain 31 peptides. Score 0.519 Round 4: 910 peptides, 111 chains. Longest chain 31 peptides. Score 0.523 Round 5: 922 peptides, 118 chains. Longest chain 25 peptides. Score 0.511 Taking the results from Round 4 Chains 121, Residues 799, Estimated correctness of the model 0.0 % 20 chains (152 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 27575 restraints for refining 12415 atoms. 24121 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2081 (Rfree = 0.000) for 12415 atoms. Found 68 (68 requested) and removed 143 (34 requested) atoms. Cycle 17: After refmac, R = 0.1934 (Rfree = 0.000) for 12271 atoms. Found 47 (67 requested) and removed 78 (33 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1853 (Rfree = 0.000) for 12203 atoms. Found 20 (67 requested) and removed 60 (33 requested) atoms. Cycle 19: After refmac, R = 0.1814 (Rfree = 0.000) for 12136 atoms. Found 20 (66 requested) and removed 54 (33 requested) atoms. Cycle 20: After refmac, R = 0.1779 (Rfree = 0.000) for 12089 atoms. Found 19 (66 requested) and removed 40 (33 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.18 Search for helices and strands: 0 residues in 0 chains, 12515 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 12531 seeds are put forward Round 1: 799 peptides, 129 chains. Longest chain 20 peptides. Score 0.397 Round 2: 893 peptides, 117 chains. Longest chain 29 peptides. Score 0.496 Round 3: 912 peptides, 118 chains. Longest chain 24 peptides. Score 0.505 Round 4: 909 peptides, 116 chains. Longest chain 30 peptides. Score 0.509 Round 5: 922 peptides, 116 chains. Longest chain 42 peptides. Score 0.517 Taking the results from Round 5 Chains 119, Residues 806, Estimated correctness of the model 0.0 % 13 chains (110 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 27898 restraints for refining 12415 atoms. 24427 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2153 (Rfree = 0.000) for 12415 atoms. Found 68 (68 requested) and removed 123 (34 requested) atoms. Cycle 22: After refmac, R = 0.1997 (Rfree = 0.000) for 12267 atoms. Found 50 (67 requested) and removed 75 (33 requested) atoms. Cycle 23: After refmac, R = 0.1932 (Rfree = 0.000) for 12198 atoms. Found 21 (67 requested) and removed 63 (33 requested) atoms. Cycle 24: After refmac, R = 0.1888 (Rfree = 0.000) for 12138 atoms. Found 16 (66 requested) and removed 56 (33 requested) atoms. Cycle 25: After refmac, R = 0.1894 (Rfree = 0.000) for 12081 atoms. Found 14 (66 requested) and removed 46 (33 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.16 Search for helices and strands: 0 residues in 0 chains, 12445 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 12475 seeds are put forward Round 1: 773 peptides, 135 chains. Longest chain 18 peptides. Score 0.359 Round 2: 856 peptides, 123 chains. Longest chain 33 peptides. Score 0.454 Round 3: 857 peptides, 117 chains. Longest chain 24 peptides. Score 0.473 Round 4: 869 peptides, 114 chains. Longest chain 29 peptides. Score 0.489 Round 5: 874 peptides, 114 chains. Longest chain 28 peptides. Score 0.492 Taking the results from Round 5 Chains 117, Residues 760, Estimated correctness of the model 0.0 % 17 chains (125 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 21461 reflections ( 96.88 % complete ) and 28077 restraints for refining 12412 atoms. 24841 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2133 (Rfree = 0.000) for 12412 atoms. Found 68 (68 requested) and removed 83 (34 requested) atoms. Cycle 27: After refmac, R = 0.1975 (Rfree = 0.000) for 12320 atoms. Found 35 (68 requested) and removed 64 (34 requested) atoms. Cycle 28: After refmac, R = 0.1853 (Rfree = 0.000) for 12256 atoms. Found 20 (67 requested) and removed 54 (33 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1796 (Rfree = 0.000) for 12206 atoms. Found 11 (67 requested) and removed 59 (33 requested) atoms. Cycle 30: After refmac, R = 0.1760 (Rfree = 0.000) for 12147 atoms. Found 13 (66 requested) and removed 50 (33 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.19 Search for helices and strands: 0 residues in 0 chains, 12557 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 12573 seeds are put forward Round 1: 789 peptides, 132 chains. Longest chain 18 peptides. Score 0.380 Round 2: 872 peptides, 118 chains. Longest chain 23 peptides. Score 0.480 Round 3: 842 peptides, 120 chains. Longest chain 19 peptides. Score 0.454 Round 4: 862 peptides, 114 chains. Longest chain 21 peptides. Score 0.485 Round 5: 856 peptides, 109 chains. Longest chain 27 peptides. Score 0.496 Taking the results from Round 5 Chains 114, Residues 747, Estimated correctness of the model 0.0 % 10 chains (103 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 27930 restraints for refining 12416 atoms. 24718 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2069 (Rfree = 0.000) for 12416 atoms. Found 68 (68 requested) and removed 74 (34 requested) atoms. Cycle 32: After refmac, R = 0.1900 (Rfree = 0.000) for 12322 atoms. Found 24 (68 requested) and removed 55 (34 requested) atoms. Cycle 33: After refmac, R = 0.1885 (Rfree = 0.000) for 12243 atoms. Found 22 (67 requested) and removed 46 (33 requested) atoms. Cycle 34: After refmac, R = 0.1794 (Rfree = 0.000) for 12188 atoms. Found 25 (67 requested) and removed 41 (33 requested) atoms. Cycle 35: After refmac, R = 0.1790 (Rfree = 0.000) for 12153 atoms. Found 30 (66 requested) and removed 47 (33 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.18 Search for helices and strands: 0 residues in 0 chains, 12603 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 12631 seeds are put forward Round 1: 717 peptides, 130 chains. Longest chain 14 peptides. Score 0.333 Round 2: 826 peptides, 119 chains. Longest chain 23 peptides. Score 0.446 Round 3: 848 peptides, 122 chains. Longest chain 21 peptides. Score 0.452 Round 4: 853 peptides, 124 chains. Longest chain 16 peptides. Score 0.449 Round 5: 861 peptides, 119 chains. Longest chain 18 peptides. Score 0.469 Taking the results from Round 5 Chains 124, Residues 742, Estimated correctness of the model 0.0 % 14 chains (83 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 28447 restraints for refining 12414 atoms. 25389 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2089 (Rfree = 0.000) for 12414 atoms. Found 52 (68 requested) and removed 62 (34 requested) atoms. Cycle 37: After refmac, R = 0.1908 (Rfree = 0.000) for 12353 atoms. Found 21 (68 requested) and removed 45 (34 requested) atoms. Cycle 38: After refmac, R = 0.1851 (Rfree = 0.000) for 12298 atoms. Found 18 (67 requested) and removed 46 (33 requested) atoms. Cycle 39: After refmac, R = 0.1823 (Rfree = 0.000) for 12247 atoms. Found 10 (67 requested) and removed 42 (33 requested) atoms. Cycle 40: After refmac, R = 0.1782 (Rfree = 0.000) for 12203 atoms. Found 14 (67 requested) and removed 40 (33 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.21 Search for helices and strands: 0 residues in 0 chains, 12670 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 12682 seeds are put forward Round 1: 700 peptides, 132 chains. Longest chain 13 peptides. Score 0.313 Round 2: 781 peptides, 124 chains. Longest chain 16 peptides. Score 0.400 Round 3: 777 peptides, 117 chains. Longest chain 18 peptides. Score 0.419 Round 4: 773 peptides, 116 chains. Longest chain 21 peptides. Score 0.419 Round 5: 814 peptides, 121 chains. Longest chain 21 peptides. Score 0.432 Taking the results from Round 5 Chains 124, Residues 693, Estimated correctness of the model 0.0 % 8 chains (48 residues) have been docked in sequence ------------------------------------------------------ 21461 reflections ( 96.88 % complete ) and 29050 restraints for refining 12414 atoms. 26247 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2111 (Rfree = 0.000) for 12414 atoms. Found 49 (68 requested) and removed 51 (34 requested) atoms. Cycle 42: After refmac, R = 0.1956 (Rfree = 0.000) for 12355 atoms. Found 25 (68 requested) and removed 43 (34 requested) atoms. Cycle 43: After refmac, R = 0.1890 (Rfree = 0.000) for 12321 atoms. Found 15 (67 requested) and removed 35 (33 requested) atoms. Cycle 44: After refmac, R = 0.1868 (Rfree = 0.000) for 12294 atoms. Found 10 (67 requested) and removed 33 (33 requested) atoms. Cycle 45: After refmac, R = 0.1828 (Rfree = 0.000) for 12266 atoms. Found 4 (67 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.19 Search for helices and strands: 0 residues in 0 chains, 12705 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 12722 seeds are put forward Round 1: 666 peptides, 126 chains. Longest chain 16 peptides. Score 0.307 Round 2: 741 peptides, 117 chains. Longest chain 18 peptides. Score 0.393 Round 3: 720 peptides, 108 chains. Longest chain 19 peptides. Score 0.407 Round 4: 729 peptides, 107 chains. Longest chain 20 peptides. Score 0.417 Round 5: 737 peptides, 107 chains. Longest chain 18 peptides. Score 0.422 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 108, Residues 630, Estimated correctness of the model 0.0 % 13 chains (74 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2p10-3_warpNtrace.pdb as input Building loops using Loopy2018 108 chains (630 residues) following loop building 13 chains (74 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 21461 reflections ( 96.88 % complete ) and 29620 restraints for refining 12417 atoms. 26978 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2016 (Rfree = 0.000) for 12417 atoms. Found 0 (68 requested) and removed 34 (34 requested) atoms. Cycle 47: After refmac, R = 0.1941 (Rfree = 0.000) for 12312 atoms. Found 0 (68 requested) and removed 34 (34 requested) atoms. Cycle 48: After refmac, R = 0.1903 (Rfree = 0.000) for 12251 atoms. Found 0 (67 requested) and removed 33 (33 requested) atoms. Cycle 49: After refmac, R = 0.1899 (Rfree = 0.000) for 12193 atoms. TimeTaking 162.8