Sun 23 Dec 22:22:41 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 2opk-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2opk-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2opk-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-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/2opk-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-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 22:22:50 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/2opk-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-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 389 and 0 Target number of residues in the AU: 389 Target solvent content: 0.6294 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 448 Adjusted target solvent content: 0.57 Input MTZ file: 2opk-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3584 target number of atoms Had to go as low as 0.85 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: 28.177 4.001 Wilson plot Bfac: 66.14 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 5294 reflections ( 99.47 % complete ) and 0 restraints for refining 3966 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3094 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3078 (Rfree = 0.000) for 3966 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.15 Search for helices and strands: 0 residues in 0 chains, 3988 seeds are put forward NCS extension: 0 residues added, 3988 seeds are put forward Round 1: 195 peptides, 33 chains. Longest chain 13 peptides. Score 0.377 Round 2: 275 peptides, 38 chains. Longest chain 20 peptides. Score 0.531 Round 3: 297 peptides, 36 chains. Longest chain 20 peptides. Score 0.601 Round 4: 320 peptides, 34 chains. Longest chain 31 peptides. Score 0.664 Round 5: 304 peptides, 37 chains. Longest chain 19 peptides. Score 0.606 Taking the results from Round 4 Chains 37, Residues 286, Estimated correctness of the model 13.6 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 6665 restraints for refining 3235 atoms. 5492 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2607 (Rfree = 0.000) for 3235 atoms. Found 15 (15 requested) and removed 34 (7 requested) atoms. Cycle 2: After refmac, R = 0.2488 (Rfree = 0.000) for 3134 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 3: After refmac, R = 0.2553 (Rfree = 0.000) for 3087 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 4: After refmac, R = 0.2428 (Rfree = 0.000) for 3056 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 5: After refmac, R = 0.2156 (Rfree = 0.000) for 3027 atoms. Found 3 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 3080 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 3106 seeds are put forward Round 1: 241 peptides, 41 chains. Longest chain 14 peptides. Score 0.409 Round 2: 294 peptides, 38 chains. Longest chain 21 peptides. Score 0.575 Round 3: 290 peptides, 39 chains. Longest chain 19 peptides. Score 0.556 Round 4: 295 peptides, 36 chains. Longest chain 24 peptides. Score 0.597 Round 5: 300 peptides, 34 chains. Longest chain 23 peptides. Score 0.626 Taking the results from Round 5 Chains 37, Residues 266, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 6786 restraints for refining 3235 atoms. 5683 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2535 (Rfree = 0.000) for 3235 atoms. Found 15 (15 requested) and removed 33 (7 requested) atoms. Cycle 7: After refmac, R = 0.2375 (Rfree = 0.000) for 3167 atoms. Found 14 (15 requested) and removed 28 (7 requested) atoms. Cycle 8: After refmac, R = 0.2129 (Rfree = 0.000) for 3126 atoms. Found 12 (14 requested) and removed 16 (7 requested) atoms. Cycle 9: After refmac, R = 0.2216 (Rfree = 0.000) for 3111 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 10: After refmac, R = 0.2174 (Rfree = 0.000) for 3096 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 3.19 Search for helices and strands: 0 residues in 0 chains, 3170 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 3192 seeds are put forward Round 1: 272 peptides, 44 chains. Longest chain 15 peptides. Score 0.458 Round 2: 305 peptides, 38 chains. Longest chain 27 peptides. Score 0.598 Round 3: 295 peptides, 39 chains. Longest chain 26 peptides. Score 0.567 Round 4: 296 peptides, 36 chains. Longest chain 21 peptides. Score 0.599 Round 5: 319 peptides, 39 chains. Longest chain 24 peptides. Score 0.618 Taking the results from Round 5 Chains 43, Residues 280, Estimated correctness of the model 0.0 % 4 chains (48 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 6531 restraints for refining 3236 atoms. 5261 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2445 (Rfree = 0.000) for 3236 atoms. Found 15 (15 requested) and removed 30 (7 requested) atoms. Cycle 12: After refmac, R = 0.2338 (Rfree = 0.000) for 3186 atoms. Found 13 (15 requested) and removed 22 (7 requested) atoms. Cycle 13: After refmac, R = 0.2270 (Rfree = 0.000) for 3161 atoms. Found 13 (15 requested) and removed 23 (7 requested) atoms. Cycle 14: After refmac, R = 0.2251 (Rfree = 0.000) for 3140 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 15: After refmac, R = 0.2132 (Rfree = 0.000) for 3129 atoms. Found 7 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.18 Search for helices and strands: 0 residues in 0 chains, 3178 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 3206 seeds are put forward Round 1: 265 peptides, 42 chains. Longest chain 13 peptides. Score 0.462 Round 2: 288 peptides, 40 chains. Longest chain 19 peptides. Score 0.541 Round 3: 282 peptides, 35 chains. Longest chain 23 peptides. Score 0.578 Round 4: 276 peptides, 38 chains. Longest chain 27 peptides. Score 0.534 Round 5: 272 peptides, 38 chains. Longest chain 16 peptides. Score 0.524 Taking the results from Round 3 Chains 35, Residues 247, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7207 restraints for refining 3237 atoms. 6254 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2584 (Rfree = 0.000) for 3237 atoms. Found 15 (15 requested) and removed 35 (7 requested) atoms. Cycle 17: After refmac, R = 0.2390 (Rfree = 0.000) for 3182 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 18: After refmac, R = 0.2071 (Rfree = 0.000) for 3162 atoms. Found 9 (15 requested) and removed 21 (7 requested) atoms. Cycle 19: After refmac, R = 0.1967 (Rfree = 0.000) for 3141 atoms. Found 5 (14 requested) and removed 12 (7 requested) atoms. Cycle 20: After refmac, R = 0.1957 (Rfree = 0.000) for 3127 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 3183 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3209 seeds are put forward Round 1: 234 peptides, 42 chains. Longest chain 15 peptides. Score 0.377 Round 2: 259 peptides, 38 chains. Longest chain 17 peptides. Score 0.492 Round 3: 254 peptides, 39 chains. Longest chain 14 peptides. Score 0.468 Round 4: 251 peptides, 37 chains. Longest chain 18 peptides. Score 0.483 Round 5: 252 peptides, 34 chains. Longest chain 15 peptides. Score 0.519 Taking the results from Round 5 Chains 34, Residues 218, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7490 restraints for refining 3236 atoms. 6652 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2611 (Rfree = 0.000) for 3236 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 22: After refmac, R = 0.2361 (Rfree = 0.000) for 3190 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 23: After refmac, R = 0.2363 (Rfree = 0.000) for 3171 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 24: After refmac, R = 0.2302 (Rfree = 0.000) for 3150 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 25: After refmac, R = 0.1819 (Rfree = 0.000) for 3138 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.15 Search for helices and strands: 0 residues in 0 chains, 3232 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3254 seeds are put forward Round 1: 202 peptides, 40 chains. Longest chain 8 peptides. Score 0.307 Round 2: 269 peptides, 43 chains. Longest chain 23 peptides. Score 0.461 Round 3: 262 peptides, 41 chains. Longest chain 17 peptides. Score 0.466 Round 4: 259 peptides, 42 chains. Longest chain 15 peptides. Score 0.446 Round 5: 254 peptides, 37 chains. Longest chain 18 peptides. Score 0.490 Taking the results from Round 5 Chains 37, Residues 217, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7313 restraints for refining 3237 atoms. 6455 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2472 (Rfree = 0.000) for 3237 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 27: After refmac, R = 0.2513 (Rfree = 0.000) for 3193 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 28: After refmac, R = 0.2082 (Rfree = 0.000) for 3170 atoms. Found 9 (15 requested) and removed 11 (7 requested) atoms. Cycle 29: After refmac, R = 0.1975 (Rfree = 0.000) for 3161 atoms. Found 8 (15 requested) and removed 13 (7 requested) atoms. Cycle 30: After refmac, R = 0.1915 (Rfree = 0.000) for 3148 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 3203 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 3234 seeds are put forward Round 1: 195 peptides, 36 chains. Longest chain 12 peptides. Score 0.337 Round 2: 231 peptides, 37 chains. Longest chain 12 peptides. Score 0.429 Round 3: 251 peptides, 40 chains. Longest chain 17 peptides. Score 0.448 Round 4: 245 peptides, 38 chains. Longest chain 11 peptides. Score 0.456 Round 5: 263 peptides, 40 chains. Longest chain 14 peptides. Score 0.480 Taking the results from Round 5 Chains 40, Residues 223, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7404 restraints for refining 3235 atoms. 6552 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2374 (Rfree = 0.000) for 3235 atoms. Found 14 (15 requested) and removed 19 (7 requested) atoms. Cycle 32: After refmac, R = 0.2495 (Rfree = 0.000) for 3201 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 33: After refmac, R = 0.2375 (Rfree = 0.000) for 3182 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 34: After refmac, R = 0.2352 (Rfree = 0.000) for 3166 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 35: After refmac, R = 0.2271 (Rfree = 0.000) for 3160 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.16 Search for helices and strands: 0 residues in 0 chains, 3235 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3248 seeds are put forward Round 1: 218 peptides, 44 chains. Longest chain 9 peptides. Score 0.304 Round 2: 247 peptides, 39 chains. Longest chain 15 peptides. Score 0.449 Round 3: 257 peptides, 39 chains. Longest chain 18 peptides. Score 0.475 Round 4: 262 peptides, 39 chains. Longest chain 15 peptides. Score 0.488 Round 5: 261 peptides, 36 chains. Longest chain 18 peptides. Score 0.519 Taking the results from Round 5 Chains 36, Residues 225, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7237 restraints for refining 3237 atoms. 6373 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2535 (Rfree = 0.000) for 3237 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 37: After refmac, R = 0.2531 (Rfree = 0.000) for 3199 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 38: After refmac, R = 0.2473 (Rfree = 0.000) for 3163 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 39: After refmac, R = 0.2507 (Rfree = 0.000) for 3151 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 40: After refmac, R = 0.2446 (Rfree = 0.000) for 3128 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 3212 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3231 seeds are put forward Round 1: 186 peptides, 37 chains. Longest chain 9 peptides. Score 0.296 Round 2: 229 peptides, 41 chains. Longest chain 17 peptides. Score 0.375 Round 3: 236 peptides, 39 chains. Longest chain 20 peptides. Score 0.419 Round 4: 235 peptides, 40 chains. Longest chain 15 peptides. Score 0.404 Round 5: 219 peptides, 37 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 3 Chains 39, Residues 197, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7376 restraints for refining 3237 atoms. 6608 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2729 (Rfree = 0.000) for 3237 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 42: After refmac, R = 0.2666 (Rfree = 0.000) for 3188 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 43: After refmac, R = 0.2650 (Rfree = 0.000) for 3162 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 44: After refmac, R = 0.2446 (Rfree = 0.000) for 3149 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 45: After refmac, R = 0.2548 (Rfree = 0.000) for 3138 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.14 Search for helices and strands: 0 residues in 0 chains, 3231 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 3261 seeds are put forward Round 1: 140 peptides, 32 chains. Longest chain 6 peptides. Score 0.211 Round 2: 194 peptides, 37 chains. Longest chain 13 peptides. Score 0.321 Round 3: 186 peptides, 36 chains. Longest chain 11 peptides. Score 0.309 Round 4: 212 peptides, 40 chains. Longest chain 9 peptides. Score 0.337 Round 5: 197 peptides, 34 chains. Longest chain 14 peptides. Score 0.370 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 163, 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 2opk-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5294 reflections ( 99.47 % complete ) and 7261 restraints for refining 3162 atoms. 6643 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2684 (Rfree = 0.000) for 3162 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2686 (Rfree = 0.000) for 3132 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2567 (Rfree = 0.000) for 3112 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2505 (Rfree = 0.000) for 3092 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... TimeTaking 55.6