Sun 23 Dec 22:22:52 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 2a3n-1.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a3n-1.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a3n-1.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-1.2-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/2a3n-1.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-1.2-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 22:23:03 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/2a3n-1.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-1.2-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 379 and 0 Target number of residues in the AU: 379 Target solvent content: 0.4033 Checking the provided sequence file Detected sequence length: 355 Maximum limit of NCS related copies: 16 Number of NCS-related molecules: 1 Adjusted target number of residues: 355 Adjusted target solvent content: 0.44 Input MTZ file: 2a3n-1.2-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: 5 Cell parameters: 81.220 102.610 49.296 90.000 123.209 90.000 Input sequence file: 2a3n-1.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2840 target number of atoms Had to go as low as 0.25 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 1 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 Loops will be built when appropriate and at the last cycle Resolution range: 56.657 1.230 Wilson plot Bfac: 8.28 97603 reflections ( 99.99 % complete ) and 0 restraints for refining 3134 atoms. Observations/parameters ratio is 7.79 ------------------------------------------------------ Starting model: R = 0.3406 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2963 (Rfree = 0.000) for 3134 atoms. Found 359 (429 requested) and removed 89 (214 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.26 1.37 Round 1: 317 peptides, 10 chains. Longest chain 78 peptides. Score 0.938 Round 2: 327 peptides, 3 chains. Longest chain 225 peptides. Score 0.968 Round 3: 326 peptides, 3 chains. Longest chain 234 peptides. Score 0.968 Round 4: 329 peptides, 1 chains. Longest chain 329 peptides. Score 0.975 Round 5: 329 peptides, 1 chains. Longest chain 329 peptides. Score 0.975 Taking the results from Round 5 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 97603 reflections ( 99.99 % complete ) and 3135 restraints for refining 3184 atoms. 458 conditional restraints added. Observations/parameters ratio is 7.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2619 (Rfree = 0.000) for 3184 atoms. Found 204 (435 requested) and removed 44 (217 requested) atoms. Cycle 2: After refmac, R = 0.2437 (Rfree = 0.000) for 3342 atoms. Found 128 (457 requested) and removed 16 (228 requested) atoms. Cycle 3: After refmac, R = 0.2312 (Rfree = 0.000) for 3440 atoms. Found 125 (472 requested) and removed 11 (236 requested) atoms. Cycle 4: After refmac, R = 0.2225 (Rfree = 0.000) for 3546 atoms. Found 102 (486 requested) and removed 12 (243 requested) atoms. Cycle 5: After refmac, R = 0.2165 (Rfree = 0.000) for 3617 atoms. Found 100 (497 requested) and removed 15 (248 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.17 1.27 Round 1: 328 peptides, 3 chains. Longest chain 124 peptides. Score 0.969 Round 2: 328 peptides, 2 chains. Longest chain 190 peptides. Score 0.972 Round 3: 330 peptides, 1 chains. Longest chain 330 peptides. Score 0.976 Round 4: 329 peptides, 2 chains. Longest chain 192 peptides. Score 0.972 Round 5: 329 peptides, 2 chains. Longest chain 272 peptides. Score 0.972 Taking the results from Round 3 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 97603 reflections ( 99.99 % complete ) and 3426 restraints for refining 3490 atoms. 736 conditional restraints added. Observations/parameters ratio is 6.99 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2252 (Rfree = 0.000) for 3490 atoms. Found 167 (477 requested) and removed 16 (238 requested) atoms. Cycle 7: After refmac, R = 0.2214 (Rfree = 0.000) for 3633 atoms. Found 110 (497 requested) and removed 10 (248 requested) atoms. Cycle 8: After refmac, R = 0.2165 (Rfree = 0.000) for 3719 atoms. Found 87 (510 requested) and removed 11 (255 requested) atoms. Cycle 9: After refmac, R = 0.2121 (Rfree = 0.000) for 3787 atoms. Found 68 (518 requested) and removed 9 (259 requested) atoms. Cycle 10: After refmac, R = 0.2083 (Rfree = 0.000) for 3832 atoms. Found 93 (525 requested) and removed 7 (262 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.17 1.27 Round 1: 327 peptides, 3 chains. Longest chain 123 peptides. Score 0.968 Round 2: 329 peptides, 1 chains. Longest chain 329 peptides. Score 0.975 Round 3: 329 peptides, 1 chains. Longest chain 329 peptides. Score 0.975 Round 4: 329 peptides, 1 chains. Longest chain 329 peptides. Score 0.975 Round 5: 329 peptides, 1 chains. Longest chain 329 peptides. Score 0.975 Taking the results from Round 5 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 97603 reflections ( 99.99 % complete ) and 3755 restraints for refining 3631 atoms. 1078 conditional restraints added. Observations/parameters ratio is 6.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2221 (Rfree = 0.000) for 3631 atoms. Found 201 (497 requested) and removed 19 (248 requested) atoms. Cycle 12: After refmac, R = 0.2219 (Rfree = 0.000) for 3804 atoms. Found 101 (521 requested) and removed 9 (260 requested) atoms. Cycle 13: After refmac, R = 0.2162 (Rfree = 0.000) for 3886 atoms. Found 92 (532 requested) and removed 3 (266 requested) atoms. Cycle 14: After refmac, R = 0.2038 (Rfree = 0.000) for 3959 atoms. Found 99 (543 requested) and removed 13 (271 requested) atoms. Cycle 15: After refmac, R = 0.2045 (Rfree = 0.000) for 4021 atoms. Found 111 (552 requested) and removed 16 (276 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.16 1.26 Round 1: 327 peptides, 3 chains. Longest chain 123 peptides. Score 0.968 Round 2: 329 peptides, 1 chains. Longest chain 329 peptides. Score 0.975 Round 3: 326 peptides, 3 chains. Longest chain 276 peptides. Score 0.968 Round 4: 327 peptides, 2 chains. Longest chain 246 peptides. Score 0.972 Round 5: 329 peptides, 1 chains. Longest chain 329 peptides. Score 0.975 Taking the results from Round 5 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 97603 reflections ( 99.99 % complete ) and 3972 restraints for refining 3757 atoms. 1295 conditional restraints added. Observations/parameters ratio is 6.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2233 (Rfree = 0.000) for 3757 atoms. Found 214 (514 requested) and removed 30 (257 requested) atoms. Cycle 17: After refmac, R = 0.2225 (Rfree = 0.000) for 3927 atoms. Found 109 (538 requested) and removed 9 (269 requested) atoms. Cycle 18: After refmac, R = 0.2073 (Rfree = 0.000) for 4011 atoms. Found 115 (550 requested) and removed 15 (275 requested) atoms. Cycle 19: After refmac, R = 0.2014 (Rfree = 0.000) for 4085 atoms. Found 124 (562 requested) and removed 17 (281 requested) atoms. Cycle 20: After refmac, R = 0.2048 (Rfree = 0.000) for 4172 atoms. Found 116 (573 requested) and removed 30 (286 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.17 1.27 Round 1: 326 peptides, 4 chains. Longest chain 124 peptides. Score 0.965 Round 2: 330 peptides, 1 chains. Longest chain 330 peptides. Score 0.976 Round 3: 329 peptides, 2 chains. Longest chain 235 peptides. Score 0.972 Round 4: 330 peptides, 1 chains. Longest chain 330 peptides. Score 0.976 Round 5: 327 peptides, 3 chains. Longest chain 277 peptides. Score 0.968 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 97603 reflections ( 99.99 % complete ) and 3976 restraints for refining 3782 atoms. 1286 conditional restraints added. Observations/parameters ratio is 6.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2201 (Rfree = 0.000) for 3782 atoms. Found 237 (517 requested) and removed 29 (258 requested) atoms. Cycle 22: After refmac, R = 0.2229 (Rfree = 0.000) for 3976 atoms. Found 129 (545 requested) and removed 21 (272 requested) atoms. Cycle 23: After refmac, R = 0.2085 (Rfree = 0.000) for 4073 atoms. Found 114 (558 requested) and removed 11 (279 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2021 (Rfree = 0.000) for 4152 atoms. Found 122 (570 requested) and removed 19 (285 requested) atoms. Cycle 25: After refmac, R = 0.2049 (Rfree = 0.000) for 4227 atoms. Found 128 (581 requested) and removed 35 (290 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.17 1.27 Round 1: 325 peptides, 4 chains. Longest chain 123 peptides. Score 0.964 Round 2: 328 peptides, 2 chains. Longest chain 191 peptides. Score 0.972 Round 3: 328 peptides, 2 chains. Longest chain 234 peptides. Score 0.972 Round 4: 325 peptides, 4 chains. Longest chain 191 peptides. Score 0.964 Round 5: 327 peptides, 3 chains. Longest chain 234 peptides. Score 0.968 Taking the results from Round 3 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 97603 reflections ( 99.99 % complete ) and 4215 restraints for refining 3866 atoms. 1554 conditional restraints added. Observations/parameters ratio is 6.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2234 (Rfree = 0.000) for 3866 atoms. Found 236 (529 requested) and removed 30 (264 requested) atoms. Cycle 27: After refmac, R = 0.2252 (Rfree = 0.000) for 4063 atoms. Found 111 (556 requested) and removed 20 (278 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2188 (Rfree = 0.000) for 4142 atoms. Found 97 (568 requested) and removed 7 (284 requested) atoms. Cycle 29: After refmac, R = 0.2052 (Rfree = 0.000) for 4223 atoms. Found 99 (578 requested) and removed 13 (289 requested) atoms. Cycle 30: After refmac, R = 0.1998 (Rfree = 0.000) for 4278 atoms. Found 120 (588 requested) and removed 31 (294 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.17 1.27 Round 1: 327 peptides, 3 chains. Longest chain 123 peptides. Score 0.968 Round 2: 328 peptides, 2 chains. Longest chain 191 peptides. Score 0.972 Round 3: 329 peptides, 1 chains. Longest chain 329 peptides. Score 0.975 Round 4: 328 peptides, 2 chains. Longest chain 191 peptides. Score 0.972 Round 5: 327 peptides, 3 chains. Longest chain 234 peptides. Score 0.968 Taking the results from Round 3 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 97603 reflections ( 99.99 % complete ) and 4271 restraints for refining 3882 atoms. 1594 conditional restraints added. Observations/parameters ratio is 6.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2208 (Rfree = 0.000) for 3882 atoms. Found 275 (531 requested) and removed 28 (265 requested) atoms. Cycle 32: After refmac, R = 0.2261 (Rfree = 0.000) for 4119 atoms. Found 123 (564 requested) and removed 16 (282 requested) atoms. Cycle 33: After refmac, R = 0.2203 (Rfree = 0.000) for 4208 atoms. Found 101 (577 requested) and removed 7 (288 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2071 (Rfree = 0.000) for 4285 atoms. Found 114 (588 requested) and removed 15 (294 requested) atoms. Cycle 35: After refmac, R = 0.2021 (Rfree = 0.000) for 4361 atoms. Found 114 (599 requested) and removed 18 (299 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.16 1.26 Round 1: 326 peptides, 4 chains. Longest chain 123 peptides. Score 0.965 Round 2: 326 peptides, 3 chains. Longest chain 235 peptides. Score 0.968 Round 3: 328 peptides, 2 chains. Longest chain 191 peptides. Score 0.972 Round 4: 328 peptides, 2 chains. Longest chain 302 peptides. Score 0.972 Round 5: 327 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 97603 reflections ( 99.99 % complete ) and 4361 restraints for refining 3958 atoms. 1698 conditional restraints added. Observations/parameters ratio is 6.16 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2247 (Rfree = 0.000) for 3958 atoms. Found 252 (542 requested) and removed 32 (271 requested) atoms. Cycle 37: After refmac, R = 0.2257 (Rfree = 0.000) for 4167 atoms. Found 147 (571 requested) and removed 8 (285 requested) atoms. Cycle 38: After refmac, R = 0.2224 (Rfree = 0.000) for 4289 atoms. Found 102 (589 requested) and removed 8 (294 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2081 (Rfree = 0.000) for 4367 atoms. Found 99 (599 requested) and removed 10 (299 requested) atoms. Cycle 40: After refmac, R = 0.2031 (Rfree = 0.000) for 4425 atoms. Found 109 (609 requested) and removed 19 (304 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.17 1.27 Round 1: 326 peptides, 3 chains. Longest chain 190 peptides. Score 0.968 Round 2: 327 peptides, 3 chains. Longest chain 235 peptides. Score 0.968 Round 3: 328 peptides, 2 chains. Longest chain 191 peptides. Score 0.972 Round 4: 329 peptides, 1 chains. Longest chain 329 peptides. Score 0.975 Round 5: 325 peptides, 5 chains. Longest chain 191 peptides. Score 0.961 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 97603 reflections ( 99.99 % complete ) and 4390 restraints for refining 3978 atoms. 1713 conditional restraints added. Observations/parameters ratio is 6.13 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2251 (Rfree = 0.000) for 3978 atoms. Found 261 (544 requested) and removed 50 (272 requested) atoms. Cycle 42: After refmac, R = 0.2274 (Rfree = 0.000) for 4178 atoms. Found 146 (572 requested) and removed 13 (286 requested) atoms. Cycle 43: After refmac, R = 0.2113 (Rfree = 0.000) for 4297 atoms. Found 109 (589 requested) and removed 12 (294 requested) atoms. Cycle 44: After refmac, R = 0.2037 (Rfree = 0.000) for 4372 atoms. Found 117 (600 requested) and removed 20 (300 requested) atoms. Cycle 45: After refmac, R = 0.2060 (Rfree = 0.000) for 4447 atoms. Found 128 (610 requested) and removed 31 (305 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.17 1.27 Round 1: 326 peptides, 3 chains. Longest chain 234 peptides. Score 0.968 Round 2: 328 peptides, 2 chains. Longest chain 191 peptides. Score 0.972 Round 3: 328 peptides, 2 chains. Longest chain 248 peptides. Score 0.972 Round 4: 325 peptides, 5 chains. Longest chain 191 peptides. Score 0.961 Round 5: 329 peptides, 1 chains. Longest chain 329 peptides. Score 0.975 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2a3n-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 97603 reflections ( 99.99 % complete ) and 4479 restraints for refining 4029 atoms. 1802 conditional restraints added. Observations/parameters ratio is 6.06 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2261 (Rfree = 0.000) for 4029 atoms. Found 0 (551 requested) and removed 1 (275 requested) atoms. Cycle 47: After refmac, R = 0.2039 (Rfree = 0.000) for 4016 atoms. Found 0 (540 requested) and removed 0 (275 requested) atoms. Cycle 48: After refmac, R = 0.1952 (Rfree = 0.000) for 4006 atoms. Found 0 (538 requested) and removed 2 (274 requested) atoms. Cycle 49: After refmac, R = 0.1901 (Rfree = 0.000) for 3995 atoms. TimeTaking 74.2