null Sun 23 Dec 22:23:09 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 1zkg-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zkg-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zkg-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-4.0-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/1zkg-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-4.0-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 22:23:18 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/1zkg-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-4.0-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 290 and 0 Target number of residues in the AU: 290 Target solvent content: 0.6778 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 424 Adjusted target solvent content: 0.53 Input MTZ file: 1zkg-4.0-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: 50.537 87.114 59.148 90.000 110.732 90.000 Input sequence file: 1zkg-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3392 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: 29.148 4.000 Wilson plot Bfac: 98.52 4114 reflections ( 99.71 % complete ) and 0 restraints for refining 3755 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3590 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3668 (Rfree = 0.000) for 3755 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.90 3.75 Search for helices and strands: 0 residues in 0 chains, 3873 seeds are put forward NCS extension: 0 residues added, 3873 seeds are put forward Round 1: 111 peptides, 22 chains. Longest chain 8 peptides. Score 0.269 Round 2: 167 peptides, 29 chains. Longest chain 15 peptides. Score 0.365 Round 3: 166 peptides, 25 chains. Longest chain 24 peptides. Score 0.422 Round 4: 176 peptides, 27 chains. Longest chain 13 peptides. Score 0.425 Round 5: 169 peptides, 23 chains. Longest chain 17 peptides. Score 0.461 Taking the results from Round 5 Chains 24, Residues 146, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 7442 restraints for refining 3063 atoms. 6830 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2864 (Rfree = 0.000) for 3063 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 2: After refmac, R = 0.2555 (Rfree = 0.000) for 3013 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 3: After refmac, R = 0.2442 (Rfree = 0.000) for 2964 atoms. Found 8 (14 requested) and removed 23 (7 requested) atoms. Cycle 4: After refmac, R = 0.2473 (Rfree = 0.000) for 2923 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 5: After refmac, R = 0.2340 (Rfree = 0.000) for 2906 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.86 3.71 Search for helices and strands: 0 residues in 0 chains, 3069 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 3091 seeds are put forward Round 1: 157 peptides, 30 chains. Longest chain 8 peptides. Score 0.314 Round 2: 176 peptides, 27 chains. Longest chain 11 peptides. Score 0.425 Round 3: 173 peptides, 25 chains. Longest chain 23 peptides. Score 0.445 Round 4: 176 peptides, 22 chains. Longest chain 23 peptides. Score 0.497 Round 5: 185 peptides, 22 chains. Longest chain 23 peptides. Score 0.523 Taking the results from Round 5 Chains 22, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6560 restraints for refining 2860 atoms. 5930 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2309 (Rfree = 0.000) for 2860 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 7: After refmac, R = 0.2255 (Rfree = 0.000) for 2830 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 8: After refmac, R = 0.2237 (Rfree = 0.000) for 2803 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 9: After refmac, R = 0.2194 (Rfree = 0.000) for 2789 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 10: After refmac, R = 0.2087 (Rfree = 0.000) for 2773 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.86 3.71 Search for helices and strands: 0 residues in 0 chains, 2944 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2966 seeds are put forward Round 1: 136 peptides, 24 chains. Longest chain 9 peptides. Score 0.332 Round 2: 163 peptides, 27 chains. Longest chain 14 peptides. Score 0.382 Round 3: 161 peptides, 24 chains. Longest chain 19 peptides. Score 0.420 Round 4: 166 peptides, 21 chains. Longest chain 26 peptides. Score 0.480 Round 5: 170 peptides, 23 chains. Longest chain 16 peptides. Score 0.464 Taking the results from Round 4 Chains 21, Residues 145, Estimated correctness of the model 0.0 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6132 restraints for refining 2881 atoms. 5446 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2402 (Rfree = 0.000) for 2881 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. Cycle 12: After refmac, R = 0.2113 (Rfree = 0.000) for 2840 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. Cycle 13: After refmac, R = 0.2039 (Rfree = 0.000) for 2811 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 14: After refmac, R = 0.1552 (Rfree = 0.000) for 2794 atoms. Found 2 (13 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.1452 (Rfree = 0.000) for 2781 atoms. Found 0 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.89 3.74 Search for helices and strands: 0 residues in 0 chains, 2925 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 2963 seeds are put forward Round 1: 161 peptides, 27 chains. Longest chain 13 peptides. Score 0.375 Round 2: 179 peptides, 28 chains. Longest chain 11 peptides. Score 0.421 Round 3: 171 peptides, 24 chains. Longest chain 12 peptides. Score 0.453 Round 4: 179 peptides, 25 chains. Longest chain 16 peptides. Score 0.464 Round 5: 172 peptides, 24 chains. Longest chain 13 peptides. Score 0.456 Taking the results from Round 4 Chains 25, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6711 restraints for refining 2950 atoms. 6120 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2314 (Rfree = 0.000) for 2950 atoms. Found 14 (14 requested) and removed 33 (7 requested) atoms. Cycle 17: After refmac, R = 0.2145 (Rfree = 0.000) for 2896 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 18: After refmac, R = 0.2212 (Rfree = 0.000) for 2872 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 19: After refmac, R = 0.2181 (Rfree = 0.000) for 2853 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 20: After refmac, R = 0.2065 (Rfree = 0.000) for 2826 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.87 3.72 Search for helices and strands: 0 residues in 0 chains, 2997 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3019 seeds are put forward Round 1: 144 peptides, 29 chains. Longest chain 13 peptides. Score 0.281 Round 2: 165 peptides, 30 chains. Longest chain 10 peptides. Score 0.343 Round 3: 171 peptides, 28 chains. Longest chain 14 peptides. Score 0.394 Round 4: 162 peptides, 27 chains. Longest chain 11 peptides. Score 0.378 Round 5: 154 peptides, 25 chains. Longest chain 12 peptides. Score 0.381 Taking the results from Round 3 Chains 28, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6432 restraints for refining 2847 atoms. 5888 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2469 (Rfree = 0.000) for 2847 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 22: After refmac, R = 0.2227 (Rfree = 0.000) for 2803 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 23: After refmac, R = 0.2316 (Rfree = 0.000) for 2774 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 24: After refmac, R = 0.2064 (Rfree = 0.000) for 2763 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.2070 (Rfree = 0.000) for 2758 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.88 3.73 Search for helices and strands: 0 residues in 0 chains, 2907 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2927 seeds are put forward Round 1: 139 peptides, 30 chains. Longest chain 10 peptides. Score 0.245 Round 2: 161 peptides, 31 chains. Longest chain 10 peptides. Score 0.313 Round 3: 167 peptides, 27 chains. Longest chain 16 peptides. Score 0.395 Round 4: 171 peptides, 28 chains. Longest chain 14 peptides. Score 0.394 Round 5: 173 peptides, 26 chains. Longest chain 15 peptides. Score 0.430 Taking the results from Round 5 Chains 26, Residues 147, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6452 restraints for refining 2878 atoms. 5890 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2342 (Rfree = 0.000) for 2878 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 27: After refmac, R = 0.2079 (Rfree = 0.000) for 2854 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 28: After refmac, R = 0.1970 (Rfree = 0.000) for 2839 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 29: After refmac, R = 0.1963 (Rfree = 0.000) for 2828 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 30: After refmac, R = 0.1936 (Rfree = 0.000) for 2820 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.87 3.72 Search for helices and strands: 0 residues in 0 chains, 2978 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2996 seeds are put forward Round 1: 145 peptides, 31 chains. Longest chain 8 peptides. Score 0.252 Round 2: 159 peptides, 32 chains. Longest chain 8 peptides. Score 0.290 Round 3: 144 peptides, 25 chains. Longest chain 12 peptides. Score 0.346 Round 4: 156 peptides, 29 chains. Longest chain 8 peptides. Score 0.326 Round 5: 158 peptides, 29 chains. Longest chain 9 peptides. Score 0.333 Taking the results from Round 3 Chains 25, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6777 restraints for refining 2894 atoms. 6326 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2268 (Rfree = 0.000) for 2894 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 32: After refmac, R = 0.2209 (Rfree = 0.000) for 2861 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 33: After refmac, R = 0.2055 (Rfree = 0.000) for 2844 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 34: After refmac, R = 0.2066 (Rfree = 0.000) for 2832 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 35: After refmac, R = 0.2031 (Rfree = 0.000) for 2817 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.86 3.71 Search for helices and strands: 0 residues in 0 chains, 2939 seeds are put forward NCS extension: 0 residues added, 2939 seeds are put forward Round 1: 124 peptides, 27 chains. Longest chain 7 peptides. Score 0.235 Round 2: 133 peptides, 26 chains. Longest chain 8 peptides. Score 0.288 Round 3: 126 peptides, 23 chains. Longest chain 9 peptides. Score 0.311 Round 4: 134 peptides, 24 chains. Longest chain 11 peptides. Score 0.325 Round 5: 144 peptides, 26 chains. Longest chain 11 peptides. Score 0.330 Taking the results from Round 5 Chains 26, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6584 restraints for refining 2831 atoms. 6138 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2323 (Rfree = 0.000) for 2831 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Cycle 37: After refmac, R = 0.2050 (Rfree = 0.000) for 2796 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 38: After refmac, R = 0.2086 (Rfree = 0.000) for 2785 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 39: After refmac, R = 0.2058 (Rfree = 0.000) for 2773 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 40: After refmac, R = 0.2039 (Rfree = 0.000) for 2769 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 3.67 Search for helices and strands: 0 residues in 0 chains, 2904 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2907 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 9 peptides. Score 0.236 Round 2: 116 peptides, 24 chains. Longest chain 11 peptides. Score 0.254 Round 3: 115 peptides, 22 chains. Longest chain 14 peptides. Score 0.285 Round 4: 116 peptides, 22 chains. Longest chain 15 peptides. Score 0.289 Round 5: 119 peptides, 22 chains. Longest chain 9 peptides. Score 0.301 Taking the results from Round 5 Chains 22, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6574 restraints for refining 2816 atoms. 6208 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1986 (Rfree = 0.000) for 2816 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 42: After refmac, R = 0.1996 (Rfree = 0.000) for 2807 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 43: After refmac, R = 0.1834 (Rfree = 0.000) for 2793 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 44: After refmac, R = 0.1925 (Rfree = 0.000) for 2789 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 45: After refmac, R = 0.1840 (Rfree = 0.000) for 2787 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.89 3.74 Search for helices and strands: 0 residues in 0 chains, 2943 seeds are put forward NCS extension: 0 residues added, 2943 seeds are put forward Round 1: 109 peptides, 25 chains. Longest chain 7 peptides. Score 0.207 Round 2: 133 peptides, 26 chains. Longest chain 9 peptides. Score 0.288 Round 3: 129 peptides, 23 chains. Longest chain 11 peptides. Score 0.322 Round 4: 121 peptides, 24 chains. Longest chain 11 peptides. Score 0.274 Round 5: 127 peptides, 24 chains. Longest chain 7 peptides. Score 0.298 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 106, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1zkg-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4114 reflections ( 99.71 % complete ) and 6504 restraints for refining 2871 atoms. 6088 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1856 (Rfree = 0.000) for 2871 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1883 (Rfree = 0.000) for 2851 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1873 (Rfree = 0.000) for 2837 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1892 (Rfree = 0.000) for 2820 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:12:03 GMT 2018 Job finished. TimeTaking 48.9 Used memory is bytes: 18404392