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 2awa-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2awa-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2awa-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-3.2-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/2awa-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-3.2-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/2awa-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-3.2-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 1241 and 0 Target number of residues in the AU: 1241 Target solvent content: 0.6294 Checking the provided sequence file Detected sequence length: 390 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1560 Adjusted target solvent content: 0.53 Input MTZ file: 2awa-3.2-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: 4 Cell parameters: 94.281 70.854 135.686 90.000 91.232 90.000 Input sequence file: 2awa-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 12480 target number of atoms Had to go as low as 0.80 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: 135.654 3.200 Wilson plot Bfac: 66.21 28833 reflections ( 96.28 % complete ) and 0 restraints for refining 13974 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3582 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3105 (Rfree = 0.000) for 13974 atoms. Found 113 (125 requested) and removed 144 (62 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.12 Search for helices and strands: 0 residues in 0 chains, 14108 seeds are put forward NCS extension: 0 residues added, 14108 seeds are put forward Round 1: 589 peptides, 123 chains. Longest chain 13 peptides. Score 0.271 Round 2: 769 peptides, 142 chains. Longest chain 15 peptides. Score 0.366 Round 3: 828 peptides, 139 chains. Longest chain 15 peptides. Score 0.429 Round 4: 852 peptides, 132 chains. Longest chain 20 peptides. Score 0.474 Round 5: 842 peptides, 140 chains. Longest chain 16 peptides. Score 0.438 Taking the results from Round 4 Chains 135, Residues 720, Estimated correctness of the model 2.7 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 25326 restraints for refining 11392 atoms. 22469 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2658 (Rfree = 0.000) for 11392 atoms. Found 61 (102 requested) and removed 71 (51 requested) atoms. Cycle 2: After refmac, R = 0.2700 (Rfree = 0.000) for 11226 atoms. Found 38 (102 requested) and removed 66 (51 requested) atoms. Cycle 3: After refmac, R = 0.2488 (Rfree = 0.000) for 11134 atoms. Found 23 (100 requested) and removed 60 (50 requested) atoms. Cycle 4: After refmac, R = 0.2455 (Rfree = 0.000) for 11058 atoms. Found 31 (99 requested) and removed 61 (49 requested) atoms. Cycle 5: After refmac, R = 0.2400 (Rfree = 0.000) for 10999 atoms. Found 26 (98 requested) and removed 56 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 11208 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 11222 seeds are put forward Round 1: 774 peptides, 146 chains. Longest chain 12 peptides. Score 0.355 Round 2: 852 peptides, 137 chains. Longest chain 18 peptides. Score 0.457 Round 3: 858 peptides, 131 chains. Longest chain 19 peptides. Score 0.483 Round 4: 865 peptides, 130 chains. Longest chain 16 peptides. Score 0.492 Round 5: 870 peptides, 125 chains. Longest chain 19 peptides. Score 0.513 Taking the results from Round 5 Chains 125, Residues 745, Estimated correctness of the model 15.5 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 25436 restraints for refining 11392 atoms. 22529 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2519 (Rfree = 0.000) for 11392 atoms. Found 69 (102 requested) and removed 97 (51 requested) atoms. Cycle 7: After refmac, R = 0.2386 (Rfree = 0.000) for 11313 atoms. Found 42 (101 requested) and removed 61 (50 requested) atoms. Cycle 8: After refmac, R = 0.2307 (Rfree = 0.000) for 11263 atoms. Found 27 (101 requested) and removed 62 (50 requested) atoms. Cycle 9: After refmac, R = 0.2625 (Rfree = 0.000) for 11207 atoms. Found 76 (100 requested) and removed 65 (50 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2097 (Rfree = 0.000) for 11191 atoms. Found 28 (100 requested) and removed 59 (50 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.06 Search for helices and strands: 0 residues in 0 chains, 11447 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 11466 seeds are put forward Round 1: 740 peptides, 140 chains. Longest chain 18 peptides. Score 0.347 Round 2: 860 peptides, 136 chains. Longest chain 16 peptides. Score 0.467 Round 3: 866 peptides, 133 chains. Longest chain 17 peptides. Score 0.482 Round 4: 858 peptides, 132 chains. Longest chain 16 peptides. Score 0.479 Round 5: 855 peptides, 127 chains. Longest chain 21 peptides. Score 0.494 Taking the results from Round 5 Chains 127, Residues 728, Estimated correctness of the model 9.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 25438 restraints for refining 11394 atoms. 22653 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2461 (Rfree = 0.000) for 11394 atoms. Found 47 (102 requested) and removed 72 (51 requested) atoms. Cycle 12: After refmac, R = 0.2373 (Rfree = 0.000) for 11332 atoms. Found 50 (102 requested) and removed 62 (51 requested) atoms. Cycle 13: After refmac, R = 0.2266 (Rfree = 0.000) for 11295 atoms. Found 39 (101 requested) and removed 60 (50 requested) atoms. Cycle 14: After refmac, R = 0.2195 (Rfree = 0.000) for 11252 atoms. Found 31 (101 requested) and removed 56 (50 requested) atoms. Cycle 15: After refmac, R = 0.2124 (Rfree = 0.000) for 11213 atoms. Found 26 (100 requested) and removed 53 (50 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 11479 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 11494 seeds are put forward Round 1: 750 peptides, 136 chains. Longest chain 15 peptides. Score 0.372 Round 2: 813 peptides, 126 chains. Longest chain 21 peptides. Score 0.464 Round 3: 821 peptides, 130 chains. Longest chain 20 peptides. Score 0.456 Round 4: 853 peptides, 128 chains. Longest chain 23 peptides. Score 0.489 Round 5: 843 peptides, 121 chains. Longest chain 20 peptides. Score 0.506 Taking the results from Round 5 Chains 121, Residues 722, Estimated correctness of the model 13.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 25220 restraints for refining 11394 atoms. 22453 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2248 (Rfree = 0.000) for 11394 atoms. Found 57 (102 requested) and removed 89 (51 requested) atoms. Cycle 17: After refmac, R = 0.2111 (Rfree = 0.000) for 11328 atoms. Found 42 (101 requested) and removed 53 (50 requested) atoms. Cycle 18: After refmac, R = 0.2089 (Rfree = 0.000) for 11293 atoms. Found 35 (101 requested) and removed 54 (50 requested) atoms. Cycle 19: After refmac, R = 0.2023 (Rfree = 0.000) for 11262 atoms. Found 21 (101 requested) and removed 53 (50 requested) atoms. Cycle 20: After refmac, R = 0.1987 (Rfree = 0.000) for 11219 atoms. Found 17 (100 requested) and removed 51 (50 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 11448 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 11479 seeds are put forward Round 1: 757 peptides, 137 chains. Longest chain 16 peptides. Score 0.375 Round 2: 831 peptides, 129 chains. Longest chain 17 peptides. Score 0.468 Round 3: 854 peptides, 128 chains. Longest chain 18 peptides. Score 0.490 Round 4: 867 peptides, 127 chains. Longest chain 20 peptides. Score 0.504 Round 5: 837 peptides, 120 chains. Longest chain 22 peptides. Score 0.504 Taking the results from Round 5 Chains 120, Residues 717, Estimated correctness of the model 12.6 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 25244 restraints for refining 11394 atoms. 22475 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2169 (Rfree = 0.000) for 11394 atoms. Found 50 (102 requested) and removed 55 (51 requested) atoms. Cycle 22: After refmac, R = 0.2041 (Rfree = 0.000) for 11357 atoms. Found 15 (102 requested) and removed 54 (51 requested) atoms. Cycle 23: After refmac, R = 0.2027 (Rfree = 0.000) for 11307 atoms. Found 22 (101 requested) and removed 53 (50 requested) atoms. Cycle 24: After refmac, R = 0.2027 (Rfree = 0.000) for 11261 atoms. Found 35 (101 requested) and removed 51 (50 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1888 (Rfree = 0.000) for 11229 atoms. Found 17 (100 requested) and removed 52 (50 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 11422 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 11443 seeds are put forward Round 1: 701 peptides, 126 chains. Longest chain 15 peptides. Score 0.366 Round 2: 797 peptides, 131 chains. Longest chain 16 peptides. Score 0.432 Round 3: 813 peptides, 126 chains. Longest chain 19 peptides. Score 0.464 Round 4: 832 peptides, 124 chains. Longest chain 17 peptides. Score 0.486 Round 5: 788 peptides, 124 chains. Longest chain 16 peptides. Score 0.451 Taking the results from Round 4 Chains 124, Residues 708, Estimated correctness of the model 6.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 25384 restraints for refining 11393 atoms. 22676 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2150 (Rfree = 0.000) for 11393 atoms. Found 49 (102 requested) and removed 55 (51 requested) atoms. Cycle 27: After refmac, R = 0.2028 (Rfree = 0.000) for 11364 atoms. Found 29 (102 requested) and removed 53 (51 requested) atoms. Cycle 28: After refmac, R = 0.1919 (Rfree = 0.000) for 11332 atoms. Found 18 (101 requested) and removed 52 (50 requested) atoms. Cycle 29: After refmac, R = 0.1890 (Rfree = 0.000) for 11279 atoms. Found 23 (101 requested) and removed 55 (50 requested) atoms. Cycle 30: After refmac, R = 0.2210 (Rfree = 0.000) for 11232 atoms. Found 85 (100 requested) and removed 58 (50 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 11470 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 11485 seeds are put forward Round 1: 694 peptides, 138 chains. Longest chain 12 peptides. Score 0.312 Round 2: 778 peptides, 132 chains. Longest chain 15 peptides. Score 0.412 Round 3: 794 peptides, 124 chains. Longest chain 15 peptides. Score 0.456 Round 4: 799 peptides, 127 chains. Longest chain 17 peptides. Score 0.449 Round 5: 827 peptides, 128 chains. Longest chain 16 peptides. Score 0.468 Taking the results from Round 5 Chains 131, Residues 699, Estimated correctness of the model 0.7 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 24890 restraints for refining 11393 atoms. 22159 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2135 (Rfree = 0.000) for 11393 atoms. Found 47 (102 requested) and removed 57 (51 requested) atoms. Cycle 32: After refmac, R = 0.1986 (Rfree = 0.000) for 11353 atoms. Found 34 (102 requested) and removed 53 (51 requested) atoms. Cycle 33: After refmac, R = 0.1962 (Rfree = 0.000) for 11325 atoms. Found 24 (101 requested) and removed 53 (50 requested) atoms. Cycle 34: After refmac, R = 0.1970 (Rfree = 0.000) for 11286 atoms. Found 30 (101 requested) and removed 54 (50 requested) atoms. Cycle 35: After refmac, R = 0.2277 (Rfree = 0.000) for 11249 atoms. Found 101 (101 requested) and removed 57 (50 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 11498 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 11518 seeds are put forward Round 1: 685 peptides, 134 chains. Longest chain 14 peptides. Score 0.320 Round 2: 740 peptides, 119 chains. Longest chain 15 peptides. Score 0.428 Round 3: 746 peptides, 125 chains. Longest chain 16 peptides. Score 0.411 Round 4: 767 peptides, 123 chains. Longest chain 17 peptides. Score 0.436 Round 5: 766 peptides, 119 chains. Longest chain 15 peptides. Score 0.451 Taking the results from Round 5 Chains 120, Residues 647, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 25386 restraints for refining 11394 atoms. 22866 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2098 (Rfree = 0.000) for 11394 atoms. Found 60 (102 requested) and removed 57 (51 requested) atoms. Cycle 37: After refmac, R = 0.1980 (Rfree = 0.000) for 11364 atoms. Found 41 (102 requested) and removed 52 (51 requested) atoms. Cycle 38: After refmac, R = 0.1959 (Rfree = 0.000) for 11345 atoms. Found 33 (101 requested) and removed 52 (50 requested) atoms. Cycle 39: After refmac, R = 0.1906 (Rfree = 0.000) for 11313 atoms. Found 20 (101 requested) and removed 51 (50 requested) atoms. Cycle 40: After refmac, R = 0.1872 (Rfree = 0.000) for 11272 atoms. Found 24 (101 requested) and removed 51 (50 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 11434 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 11452 seeds are put forward Round 1: 648 peptides, 126 chains. Longest chain 12 peptides. Score 0.317 Round 2: 721 peptides, 126 chains. Longest chain 14 peptides. Score 0.385 Round 3: 761 peptides, 122 chains. Longest chain 17 peptides. Score 0.435 Round 4: 761 peptides, 123 chains. Longest chain 18 peptides. Score 0.431 Round 5: 774 peptides, 121 chains. Longest chain 15 peptides. Score 0.450 Taking the results from Round 5 Chains 121, Residues 653, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 28833 reflections ( 96.28 % complete ) and 25194 restraints for refining 11391 atoms. 22703 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2049 (Rfree = 0.000) for 11391 atoms. Found 35 (102 requested) and removed 53 (51 requested) atoms. Cycle 42: After refmac, R = 0.1955 (Rfree = 0.000) for 11354 atoms. Found 27 (102 requested) and removed 51 (51 requested) atoms. Cycle 43: After refmac, R = 0.1972 (Rfree = 0.000) for 11315 atoms. Found 27 (101 requested) and removed 51 (50 requested) atoms. Cycle 44: After refmac, R = 0.1900 (Rfree = 0.000) for 11281 atoms. Found 27 (101 requested) and removed 51 (50 requested) atoms. Cycle 45: After refmac, R = 0.1871 (Rfree = 0.000) for 11238 atoms. Found 16 (101 requested) and removed 52 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 11383 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 11398 seeds are put forward Round 1: 648 peptides, 124 chains. Longest chain 21 peptides. Score 0.325 Round 2: 698 peptides, 117 chains. Longest chain 19 peptides. Score 0.399 Round 3: 709 peptides, 117 chains. Longest chain 15 peptides. Score 0.409 Round 4: 740 peptides, 115 chains. Longest chain 16 peptides. Score 0.443 Round 5: 710 peptides, 113 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 115, Residues 625, 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 2awa-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 28833 reflections ( 96.28 % complete ) and 25581 restraints for refining 11394 atoms. 23196 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2002 (Rfree = 0.000) for 11394 atoms. Found 0 (102 requested) and removed 51 (51 requested) atoms. Cycle 47: After refmac, R = 0.1956 (Rfree = 0.000) for 11329 atoms. Found 0 (101 requested) and removed 50 (50 requested) atoms. Cycle 48: After refmac, R = 0.1918 (Rfree = 0.000) for 11272 atoms. Found 0 (101 requested) and removed 50 (50 requested) atoms. Cycle 49: After refmac, R = 0.1863 (Rfree = 0.000) for 11217 atoms. Found 0 (100 requested) and removed 50 (50 requested) atoms. Writing output files ... TimeTaking 135.97