Sun 23 Dec 22:23:08 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 1vlm-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlm-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlm-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-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/1vlm-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-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/1vlm-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-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 274 and 0 Target number of residues in the AU: 274 Target solvent content: 0.6600 Checking the provided sequence file Detected sequence length: 219 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 438 Adjusted target solvent content: 0.46 Input MTZ file: 1vlm-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: 18 Cell parameters: 65.648 70.734 93.922 90.000 90.000 90.000 Input sequence file: 1vlm-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3504 target number of atoms Had to go as low as 0.70 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: 93.922 4.000 Wilson plot Bfac: 84.48 3984 reflections ( 99.60 % complete ) and 0 restraints for refining 3857 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3464 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3211 (Rfree = 0.000) for 3857 atoms. Found 18 (18 requested) and removed 86 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 3.88 Search for helices and strands: 0 residues in 0 chains, 3838 seeds are put forward NCS extension: 0 residues added, 3838 seeds are put forward Round 1: 120 peptides, 26 chains. Longest chain 7 peptides. Score 0.241 Round 2: 170 peptides, 29 chains. Longest chain 17 peptides. Score 0.393 Round 3: 191 peptides, 28 chains. Longest chain 18 peptides. Score 0.483 Round 4: 191 peptides, 29 chains. Longest chain 12 peptides. Score 0.468 Round 5: 221 peptides, 31 chains. Longest chain 21 peptides. Score 0.536 Taking the results from Round 5 Chains 31, Residues 190, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 7434 restraints for refining 3157 atoms. 6705 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2749 (Rfree = 0.000) for 3157 atoms. Found 10 (15 requested) and removed 41 (7 requested) atoms. Cycle 2: After refmac, R = 0.2471 (Rfree = 0.000) for 3040 atoms. Found 4 (14 requested) and removed 31 (7 requested) atoms. Cycle 3: After refmac, R = 0.2303 (Rfree = 0.000) for 2958 atoms. Found 0 (14 requested) and removed 17 (7 requested) atoms. Cycle 4: After refmac, R = 0.2306 (Rfree = 0.000) for 2919 atoms. Found 3 (13 requested) and removed 14 (6 requested) atoms. Cycle 5: After refmac, R = 0.2509 (Rfree = 0.000) for 2882 atoms. Found 9 (13 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 4.03 Search for helices and strands: 0 residues in 0 chains, 2980 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 3012 seeds are put forward Round 1: 153 peptides, 31 chains. Longest chain 9 peptides. Score 0.293 Round 2: 179 peptides, 28 chains. Longest chain 21 peptides. Score 0.441 Round 3: 195 peptides, 28 chains. Longest chain 17 peptides. Score 0.496 Round 4: 207 peptides, 30 chains. Longest chain 17 peptides. Score 0.506 Round 5: 211 peptides, 28 chains. Longest chain 18 peptides. Score 0.546 Taking the results from Round 5 Chains 28, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6712 restraints for refining 2924 atoms. 6008 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2715 (Rfree = 0.000) for 2924 atoms. Found 12 (13 requested) and removed 31 (6 requested) atoms. Cycle 7: After refmac, R = 0.2390 (Rfree = 0.000) for 2884 atoms. Found 11 (13 requested) and removed 26 (6 requested) atoms. Cycle 8: After refmac, R = 0.2239 (Rfree = 0.000) for 2850 atoms. Found 6 (13 requested) and removed 13 (6 requested) atoms. Cycle 9: After refmac, R = 0.2118 (Rfree = 0.000) for 2827 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. Cycle 10: After refmac, R = 0.2024 (Rfree = 0.000) for 2808 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.93 Search for helices and strands: 0 residues in 0 chains, 2905 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2929 seeds are put forward Round 1: 174 peptides, 32 chains. Longest chain 16 peptides. Score 0.359 Round 2: 208 peptides, 31 chains. Longest chain 22 peptides. Score 0.495 Round 3: 200 peptides, 32 chains. Longest chain 14 peptides. Score 0.454 Round 4: 197 peptides, 31 chains. Longest chain 16 peptides. Score 0.458 Round 5: 225 peptides, 32 chains. Longest chain 23 peptides. Score 0.535 Taking the results from Round 5 Chains 33, Residues 193, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6808 restraints for refining 3027 atoms. 6035 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2594 (Rfree = 0.000) for 3027 atoms. Found 6 (14 requested) and removed 41 (7 requested) atoms. Cycle 12: After refmac, R = 0.2215 (Rfree = 0.000) for 2940 atoms. Found 2 (14 requested) and removed 13 (7 requested) atoms. Cycle 13: After refmac, R = 0.1927 (Rfree = 0.000) for 2917 atoms. Found 2 (13 requested) and removed 15 (6 requested) atoms. Cycle 14: After refmac, R = 0.1896 (Rfree = 0.000) for 2900 atoms. Found 0 (13 requested) and removed 14 (6 requested) atoms. Cycle 15: After refmac, R = 0.1794 (Rfree = 0.000) for 2883 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.73 3.93 Search for helices and strands: 0 residues in 0 chains, 2980 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2994 seeds are put forward Round 1: 161 peptides, 32 chains. Longest chain 8 peptides. Score 0.308 Round 2: 182 peptides, 31 chains. Longest chain 15 peptides. Score 0.405 Round 3: 184 peptides, 28 chains. Longest chain 13 peptides. Score 0.459 Round 4: 191 peptides, 29 chains. Longest chain 11 peptides. Score 0.468 Round 5: 188 peptides, 30 chains. Longest chain 12 peptides. Score 0.442 Taking the results from Round 4 Chains 29, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 7022 restraints for refining 3037 atoms. 6403 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2680 (Rfree = 0.000) for 3037 atoms. Found 14 (14 requested) and removed 35 (7 requested) atoms. Cycle 17: After refmac, R = 0.2344 (Rfree = 0.000) for 2976 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 18: After refmac, R = 0.2269 (Rfree = 0.000) for 2932 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 19: After refmac, R = 0.2193 (Rfree = 0.000) for 2917 atoms. Found 8 (13 requested) and removed 15 (6 requested) atoms. Cycle 20: After refmac, R = 0.2091 (Rfree = 0.000) for 2895 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.88 Search for helices and strands: 0 residues in 0 chains, 3017 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 3025 seeds are put forward Round 1: 135 peptides, 31 chains. Longest chain 6 peptides. Score 0.216 Round 2: 162 peptides, 30 chains. Longest chain 10 peptides. Score 0.346 Round 3: 172 peptides, 30 chains. Longest chain 13 peptides. Score 0.384 Round 4: 168 peptides, 31 chains. Longest chain 13 peptides. Score 0.353 Round 5: 173 peptides, 31 chains. Longest chain 16 peptides. Score 0.372 Taking the results from Round 3 Chains 30, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6508 restraints for refining 2849 atoms. 5970 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2573 (Rfree = 0.000) for 2849 atoms. Found 11 (13 requested) and removed 20 (6 requested) atoms. Cycle 22: After refmac, R = 0.2189 (Rfree = 0.000) for 2822 atoms. Found 12 (13 requested) and removed 14 (6 requested) atoms. Cycle 23: After refmac, R = 0.2015 (Rfree = 0.000) for 2812 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. Cycle 24: After refmac, R = 0.2078 (Rfree = 0.000) for 2807 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.2099 (Rfree = 0.000) for 2802 atoms. Found 10 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 3.99 Search for helices and strands: 0 residues in 0 chains, 2873 seeds are put forward NCS extension: 0 residues added, 2873 seeds are put forward Round 1: 134 peptides, 29 chains. Longest chain 8 peptides. Score 0.248 Round 2: 182 peptides, 34 chains. Longest chain 10 peptides. Score 0.357 Round 3: 177 peptides, 33 chains. Longest chain 9 peptides. Score 0.354 Round 4: 180 peptides, 31 chains. Longest chain 12 peptides. Score 0.398 Round 5: 174 peptides, 27 chains. Longest chain 13 peptides. Score 0.439 Taking the results from Round 5 Chains 27, Residues 147, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6635 restraints for refining 2914 atoms. 6074 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2410 (Rfree = 0.000) for 2914 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 27: After refmac, R = 0.2175 (Rfree = 0.000) for 2881 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 28: After refmac, R = 0.1944 (Rfree = 0.000) for 2867 atoms. Found 6 (13 requested) and removed 12 (6 requested) atoms. Cycle 29: After refmac, R = 0.2067 (Rfree = 0.000) for 2858 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 30: After refmac, R = 0.1739 (Rfree = 0.000) for 2856 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.95 Search for helices and strands: 0 residues in 0 chains, 2943 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 2957 seeds are put forward Round 1: 121 peptides, 27 chains. Longest chain 7 peptides. Score 0.227 Round 2: 149 peptides, 27 chains. Longest chain 9 peptides. Score 0.345 Round 3: 155 peptides, 29 chains. Longest chain 9 peptides. Score 0.335 Round 4: 158 peptides, 27 chains. Longest chain 11 peptides. Score 0.380 Round 5: 142 peptides, 25 chains. Longest chain 9 peptides. Score 0.352 Taking the results from Round 4 Chains 27, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6566 restraints for refining 2859 atoms. 6069 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2249 (Rfree = 0.000) for 2859 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 32: After refmac, R = 0.1960 (Rfree = 0.000) for 2835 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 33: After refmac, R = 0.1876 (Rfree = 0.000) for 2827 atoms. Found 5 (13 requested) and removed 16 (6 requested) atoms. Cycle 34: After refmac, R = 0.1405 (Rfree = 0.000) for 2814 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.1328 (Rfree = 0.000) for 2809 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.91 Search for helices and strands: 0 residues in 0 chains, 2886 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 2896 seeds are put forward Round 1: 130 peptides, 29 chains. Longest chain 7 peptides. Score 0.231 Round 2: 154 peptides, 30 chains. Longest chain 9 peptides. Score 0.314 Round 3: 163 peptides, 30 chains. Longest chain 8 peptides. Score 0.350 Round 4: 168 peptides, 29 chains. Longest chain 10 peptides. Score 0.385 Round 5: 163 peptides, 30 chains. Longest chain 10 peptides. Score 0.350 Taking the results from Round 4 Chains 29, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6542 restraints for refining 2894 atoms. 6015 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1732 (Rfree = 0.000) for 2894 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 37: After refmac, R = 0.1660 (Rfree = 0.000) for 2882 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.1646 (Rfree = 0.000) for 2874 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1311 (Rfree = 0.000) for 2872 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1417 (Rfree = 0.000) for 2855 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 3.93 Search for helices and strands: 0 residues in 0 chains, 2933 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2936 seeds are put forward Round 1: 123 peptides, 27 chains. Longest chain 8 peptides. Score 0.236 Round 2: 128 peptides, 27 chains. Longest chain 7 peptides. Score 0.258 Round 3: 151 peptides, 28 chains. Longest chain 8 peptides. Score 0.336 Round 4: 143 peptides, 28 chains. Longest chain 8 peptides. Score 0.304 Round 5: 151 peptides, 25 chains. Longest chain 13 peptides. Score 0.387 Taking the results from Round 5 Chains 25, Residues 126, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6666 restraints for refining 2982 atoms. 6127 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2429 (Rfree = 0.000) for 2982 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 42: After refmac, R = 0.2351 (Rfree = 0.000) for 2956 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 43: After refmac, R = 0.1813 (Rfree = 0.000) for 2934 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.1830 (Rfree = 0.000) for 2912 atoms. Found 7 (13 requested) and removed 12 (6 requested) atoms. Cycle 45: After refmac, R = 0.2004 (Rfree = 0.000) for 2897 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.88 Search for helices and strands: 0 residues in 0 chains, 2970 seeds are put forward NCS extension: 0 residues added, 2970 seeds are put forward Round 1: 104 peptides, 21 chains. Longest chain 9 peptides. Score 0.264 Round 2: 129 peptides, 27 chains. Longest chain 7 peptides. Score 0.263 Round 3: 131 peptides, 25 chains. Longest chain 9 peptides. Score 0.307 Round 4: 125 peptides, 24 chains. Longest chain 9 peptides. Score 0.300 Round 5: 145 peptides, 27 chains. Longest chain 10 peptides. Score 0.329 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 118, 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 1vlm-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3984 reflections ( 99.60 % complete ) and 6469 restraints for refining 2821 atoms. 6024 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2256 (Rfree = 0.000) for 2821 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2054 (Rfree = 0.000) for 2803 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2264 (Rfree = 0.000) for 2789 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2038 (Rfree = 0.000) for 2773 atoms. TimeTaking 49.45