Sun 23 Dec 22:22:59 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 2gvk-1.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gvk-1.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gvk-1.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-1.6-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/2gvk-1.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-1.6-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 22:23:07 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/2gvk-1.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-1.6-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 464 and 0 Target number of residues in the AU: 464 Target solvent content: 0.4029 Checking the provided sequence file Detected sequence length: 317 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 317 Adjusted target solvent content: 0.59 Input MTZ file: 2gvk-1.6-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: 182 Cell parameters: 109.180 109.180 122.210 90.000 90.000 120.000 Input sequence file: 2gvk-1.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2536 target number of atoms Had to go as low as 0.40 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: 29.072 1.600 Wilson plot Bfac: 8.25 56929 reflections ( 99.69 % complete ) and 0 restraints for refining 2804 atoms. Observations/parameters ratio is 5.08 ------------------------------------------------------ Starting model: R = 0.3088 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2658 (Rfree = 0.000) for 2804 atoms. Found 181 (181 requested) and removed 89 (90 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.59 1.41 Round 1: 277 peptides, 14 chains. Longest chain 67 peptides. Score 0.840 Round 2: 293 peptides, 8 chains. Longest chain 130 peptides. Score 0.895 Round 3: 296 peptides, 7 chains. Longest chain 216 peptides. Score 0.904 Round 4: 297 peptides, 6 chains. Longest chain 142 peptides. Score 0.910 Round 5: 298 peptides, 9 chains. Longest chain 126 peptides. Score 0.894 Taking the results from Round 4 Chains 6, Residues 291, Estimated correctness of the model 99.6 % 4 chains (279 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 162 A and 167 A Built loop between residues 238 A and 249 A Built loop between residues 284 A and 287 A 2 chains (302 residues) following loop building 1 chains (295 residues) in sequence following loop building ------------------------------------------------------ 56929 reflections ( 99.69 % complete ) and 2805 restraints for refining 2787 atoms. 419 conditional restraints added. Observations/parameters ratio is 5.11 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2741 (Rfree = 0.000) for 2787 atoms. Found 145 (180 requested) and removed 21 (90 requested) atoms. Cycle 2: After refmac, R = 0.2533 (Rfree = 0.000) for 2910 atoms. Found 129 (188 requested) and removed 12 (94 requested) atoms. Cycle 3: After refmac, R = 0.2465 (Rfree = 0.000) for 3017 atoms. Found 108 (195 requested) and removed 29 (97 requested) atoms. Cycle 4: After refmac, R = 0.2413 (Rfree = 0.000) for 3094 atoms. Found 87 (200 requested) and removed 20 (100 requested) atoms. Cycle 5: After refmac, R = 0.2380 (Rfree = 0.000) for 3153 atoms. Found 89 (204 requested) and removed 19 (102 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.53 1.36 Round 1: 295 peptides, 9 chains. Longest chain 86 peptides. Score 0.892 Round 2: 297 peptides, 7 chains. Longest chain 88 peptides. Score 0.904 Round 3: 300 peptides, 5 chains. Longest chain 218 peptides. Score 0.917 Round 4: 299 peptides, 6 chains. Longest chain 86 peptides. Score 0.911 Round 5: 296 peptides, 8 chains. Longest chain 125 peptides. Score 0.898 Taking the results from Round 3 Chains 6, Residues 295, Estimated correctness of the model 99.6 % 4 chains (287 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 238 A and 242 A Built loop between residues 283 A and 287 A Built loop between residues 299 A and 302 A 2 chains (302 residues) following loop building 1 chains (295 residues) in sequence following loop building ------------------------------------------------------ 56929 reflections ( 99.69 % complete ) and 2963 restraints for refining 3000 atoms. 577 conditional restraints added. Observations/parameters ratio is 4.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2405 (Rfree = 0.000) for 3000 atoms. Found 156 (194 requested) and removed 27 (97 requested) atoms. Cycle 7: After refmac, R = 0.2389 (Rfree = 0.000) for 3123 atoms. Found 110 (202 requested) and removed 19 (101 requested) atoms. Cycle 8: After refmac, R = 0.2334 (Rfree = 0.000) for 3211 atoms. Found 87 (207 requested) and removed 14 (103 requested) atoms. Cycle 9: After refmac, R = 0.2322 (Rfree = 0.000) for 3275 atoms. Found 87 (212 requested) and removed 29 (106 requested) atoms. Cycle 10: After refmac, R = 0.2325 (Rfree = 0.000) for 3322 atoms. Found 111 (215 requested) and removed 37 (107 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.52 1.35 Round 1: 295 peptides, 8 chains. Longest chain 125 peptides. Score 0.897 Round 2: 296 peptides, 7 chains. Longest chain 86 peptides. Score 0.904 Round 3: 298 peptides, 6 chains. Longest chain 173 peptides. Score 0.910 Round 4: 299 peptides, 5 chains. Longest chain 140 peptides. Score 0.916 Round 5: 296 peptides, 9 chains. Longest chain 87 peptides. Score 0.893 Taking the results from Round 4 Chains 5, Residues 294, Estimated correctness of the model 99.6 % 4 chains (287 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 105 A and 108 A Built loop between residues 246 A and 250 A Built loop between residues 283 A and 286 A 2 chains (301 residues) following loop building 1 chains (294 residues) in sequence following loop building ------------------------------------------------------ 56929 reflections ( 99.69 % complete ) and 3092 restraints for refining 3113 atoms. 710 conditional restraints added. Observations/parameters ratio is 4.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2398 (Rfree = 0.000) for 3113 atoms. Found 165 (201 requested) and removed 37 (100 requested) atoms. Cycle 12: After refmac, R = 0.2391 (Rfree = 0.000) for 3234 atoms. Found 106 (209 requested) and removed 21 (104 requested) atoms. Cycle 13: After refmac, R = 0.2363 (Rfree = 0.000) for 3313 atoms. Found 90 (214 requested) and removed 24 (107 requested) atoms. Cycle 14: After refmac, R = 0.2348 (Rfree = 0.000) for 3372 atoms. Found 97 (218 requested) and removed 39 (109 requested) atoms. Cycle 15: After refmac, R = 0.2328 (Rfree = 0.000) for 3420 atoms. Found 102 (221 requested) and removed 27 (110 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.52 1.35 Round 1: 293 peptides, 9 chains. Longest chain 85 peptides. Score 0.890 Round 2: 296 peptides, 7 chains. Longest chain 87 peptides. Score 0.904 Round 3: 297 peptides, 7 chains. Longest chain 89 peptides. Score 0.904 Round 4: 295 peptides, 6 chains. Longest chain 173 peptides. Score 0.908 Round 5: 297 peptides, 7 chains. Longest chain 85 peptides. Score 0.904 Taking the results from Round 4 Chains 6, Residues 289, Estimated correctness of the model 99.6 % 5 chains (282 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 75 A Built loop between residues 246 A and 253 A Built loop between residues 283 A and 286 A Built loop between residues 299 A and 302 A 2 chains (301 residues) following loop building 1 chains (294 residues) in sequence following loop building ------------------------------------------------------ 56929 reflections ( 99.69 % complete ) and 3172 restraints for refining 3174 atoms. 790 conditional restraints added. Observations/parameters ratio is 4.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2401 (Rfree = 0.000) for 3174 atoms. Found 190 (205 requested) and removed 28 (102 requested) atoms. Cycle 17: After refmac, R = 0.2428 (Rfree = 0.000) for 3330 atoms. Found 102 (215 requested) and removed 34 (107 requested) atoms. Cycle 18: After refmac, R = 0.2376 (Rfree = 0.000) for 3387 atoms. Found 107 (219 requested) and removed 25 (109 requested) atoms. Cycle 19: After refmac, R = 0.2358 (Rfree = 0.000) for 3461 atoms. Found 80 (224 requested) and removed 33 (112 requested) atoms. Cycle 20: After refmac, R = 0.2342 (Rfree = 0.000) for 3483 atoms. Found 93 (226 requested) and removed 27 (113 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.51 1.34 Round 1: 296 peptides, 8 chains. Longest chain 85 peptides. Score 0.898 Round 2: 297 peptides, 7 chains. Longest chain 87 peptides. Score 0.904 Round 3: 300 peptides, 4 chains. Longest chain 225 peptides. Score 0.922 Round 4: 298 peptides, 7 chains. Longest chain 86 peptides. Score 0.905 Round 5: 301 peptides, 5 chains. Longest chain 117 peptides. Score 0.918 Taking the results from Round 3 Chains 4, Residues 296, Estimated correctness of the model 99.7 % 3 chains (289 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 246 A and 250 A Built loop between residues 283 A and 286 A 2 chains (301 residues) following loop building 1 chains (294 residues) in sequence following loop building ------------------------------------------------------ 56929 reflections ( 99.69 % complete ) and 3279 restraints for refining 3218 atoms. 897 conditional restraints added. Observations/parameters ratio is 4.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2396 (Rfree = 0.000) for 3218 atoms. Found 191 (208 requested) and removed 31 (104 requested) atoms. Cycle 22: After refmac, R = 0.2401 (Rfree = 0.000) for 3371 atoms. Found 105 (218 requested) and removed 44 (109 requested) atoms. Cycle 23: After refmac, R = 0.2335 (Rfree = 0.000) for 3424 atoms. Found 78 (222 requested) and removed 27 (111 requested) atoms. Cycle 24: After refmac, R = 0.2296 (Rfree = 0.000) for 3465 atoms. Found 84 (224 requested) and removed 29 (112 requested) atoms. Cycle 25: After refmac, R = 0.2265 (Rfree = 0.000) for 3514 atoms. Found 76 (227 requested) and removed 23 (113 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.52 1.35 Round 1: 295 peptides, 8 chains. Longest chain 125 peptides. Score 0.897 Round 2: 293 peptides, 6 chains. Longest chain 129 peptides. Score 0.906 Round 3: 292 peptides, 7 chains. Longest chain 154 peptides. Score 0.900 Round 4: 297 peptides, 6 chains. Longest chain 157 peptides. Score 0.910 Round 5: 292 peptides, 8 chains. Longest chain 85 peptides. Score 0.895 Taking the results from Round 4 Chains 6, Residues 291, Estimated correctness of the model 99.6 % 4 chains (279 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 178 A and 181 A Built loop between residues 284 A and 287 A 4 chains (295 residues) following loop building 2 chains (283 residues) in sequence following loop building ------------------------------------------------------ 56929 reflections ( 99.69 % complete ) and 3485 restraints for refining 3239 atoms. 1169 conditional restraints added. Observations/parameters ratio is 4.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2384 (Rfree = 0.000) for 3239 atoms. Found 173 (209 requested) and removed 33 (104 requested) atoms. Cycle 27: After refmac, R = 0.2357 (Rfree = 0.000) for 3377 atoms. Found 103 (218 requested) and removed 16 (109 requested) atoms. Cycle 28: After refmac, R = 0.2332 (Rfree = 0.000) for 3454 atoms. Found 81 (224 requested) and removed 26 (112 requested) atoms. Cycle 29: After refmac, R = 0.2307 (Rfree = 0.000) for 3498 atoms. Found 95 (227 requested) and removed 29 (113 requested) atoms. Cycle 30: After refmac, R = 0.2285 (Rfree = 0.000) for 3552 atoms. Found 83 (230 requested) and removed 42 (115 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.51 1.34 Round 1: 294 peptides, 9 chains. Longest chain 86 peptides. Score 0.891 Round 2: 291 peptides, 5 chains. Longest chain 214 peptides. Score 0.910 Round 3: 297 peptides, 6 chains. Longest chain 155 peptides. Score 0.910 Round 4: 296 peptides, 7 chains. Longest chain 131 peptides. Score 0.904 Round 5: 294 peptides, 6 chains. Longest chain 131 peptides. Score 0.907 Taking the results from Round 3 Chains 6, Residues 291, Estimated correctness of the model 99.6 % 4 chains (280 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 175 A and 178 A Built loop between residues 283 A and 286 A 4 chains (295 residues) following loop building 2 chains (284 residues) in sequence following loop building ------------------------------------------------------ 56929 reflections ( 99.69 % complete ) and 3484 restraints for refining 3265 atoms. 1168 conditional restraints added. Observations/parameters ratio is 4.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2391 (Rfree = 0.000) for 3265 atoms. Found 190 (207 requested) and removed 29 (105 requested) atoms. Cycle 32: After refmac, R = 0.2392 (Rfree = 0.000) for 3411 atoms. Found 94 (217 requested) and removed 28 (110 requested) atoms. Cycle 33: After refmac, R = 0.2330 (Rfree = 0.000) for 3470 atoms. Found 98 (220 requested) and removed 19 (112 requested) atoms. Cycle 34: After refmac, R = 0.2281 (Rfree = 0.000) for 3540 atoms. Found 72 (224 requested) and removed 37 (114 requested) atoms. Cycle 35: After refmac, R = 0.2263 (Rfree = 0.000) for 3564 atoms. Found 82 (222 requested) and removed 31 (115 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.50 1.33 Round 1: 295 peptides, 8 chains. Longest chain 125 peptides. Score 0.897 Round 2: 295 peptides, 8 chains. Longest chain 87 peptides. Score 0.897 Round 3: 293 peptides, 7 chains. Longest chain 131 peptides. Score 0.901 Round 4: 296 peptides, 7 chains. Longest chain 124 peptides. Score 0.904 Round 5: 293 peptides, 8 chains. Longest chain 104 peptides. Score 0.895 Taking the results from Round 4 Chains 7, Residues 289, Estimated correctness of the model 99.5 % 4 chains (273 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 106 A and 109 A Built loop between residues 283 A and 286 A 5 chains (293 residues) following loop building 2 chains (277 residues) in sequence following loop building ------------------------------------------------------ 56929 reflections ( 99.69 % complete ) and 3635 restraints for refining 3278 atoms. 1354 conditional restraints added. Observations/parameters ratio is 4.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2393 (Rfree = 0.000) for 3278 atoms. Found 187 (204 requested) and removed 28 (106 requested) atoms. Cycle 37: After refmac, R = 0.2391 (Rfree = 0.000) for 3426 atoms. Found 110 (213 requested) and removed 20 (111 requested) atoms. Cycle 38: After refmac, R = 0.2343 (Rfree = 0.000) for 3506 atoms. Found 95 (218 requested) and removed 24 (113 requested) atoms. Cycle 39: After refmac, R = 0.2317 (Rfree = 0.000) for 3570 atoms. Found 68 (222 requested) and removed 36 (115 requested) atoms. Cycle 40: After refmac, R = 0.2289 (Rfree = 0.000) for 3587 atoms. Found 80 (219 requested) and removed 25 (116 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.50 1.33 Round 1: 295 peptides, 8 chains. Longest chain 124 peptides. Score 0.897 Round 2: 297 peptides, 5 chains. Longest chain 219 peptides. Score 0.915 Round 3: 299 peptides, 6 chains. Longest chain 133 peptides. Score 0.911 Round 4: 298 peptides, 7 chains. Longest chain 133 peptides. Score 0.905 Round 5: 299 peptides, 6 chains. Longest chain 133 peptides. Score 0.911 Taking the results from Round 2 Chains 5, Residues 292, Estimated correctness of the model 99.6 % 3 chains (280 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 283 A and 286 A 4 chains (294 residues) following loop building 2 chains (282 residues) in sequence following loop building ------------------------------------------------------ 56929 reflections ( 99.69 % complete ) and 3702 restraints for refining 3333 atoms. 1403 conditional restraints added. Observations/parameters ratio is 4.27 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2397 (Rfree = 0.000) for 3333 atoms. Found 195 (202 requested) and removed 25 (107 requested) atoms. Cycle 42: After refmac, R = 0.2394 (Rfree = 0.000) for 3500 atoms. Found 110 (212 requested) and removed 27 (113 requested) atoms. Cycle 43: After refmac, R = 0.2356 (Rfree = 0.000) for 3578 atoms. Found 83 (217 requested) and removed 28 (115 requested) atoms. Cycle 44: After refmac, R = 0.2328 (Rfree = 0.000) for 3617 atoms. Found 77 (221 requested) and removed 35 (117 requested) atoms. Cycle 45: After refmac, R = 0.2305 (Rfree = 0.000) for 3642 atoms. Found 98 (222 requested) and removed 35 (118 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.50 1.33 Round 1: 289 peptides, 9 chains. Longest chain 125 peptides. Score 0.886 Round 2: 297 peptides, 7 chains. Longest chain 104 peptides. Score 0.904 Round 3: 296 peptides, 8 chains. Longest chain 125 peptides. Score 0.898 Round 4: 298 peptides, 6 chains. Longest chain 133 peptides. Score 0.910 Round 5: 294 peptides, 6 chains. Longest chain 132 peptides. Score 0.907 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 292, Estimated correctness of the model 99.6 % 4 chains (281 residues) have been docked in sequence Sequence coverage is 95 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 105 A and 108 A Built loop between residues 239 A and 250 A Built loop between residues 283 A and 286 A 2 chains (302 residues) following loop building 1 chains (295 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 56929 reflections ( 99.69 % complete ) and 2386 restraints for refining 2333 atoms. Observations/parameters ratio is 6.10 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2864 (Rfree = 0.000) for 2333 atoms. Found 118 (141 requested) and removed 0 (141 requested) atoms. Cycle 47: After refmac, R = 0.2645 (Rfree = 0.000) for 2333 atoms. Found 50 (149 requested) and removed 0 (79 requested) atoms. Cycle 48: After refmac, R = 0.2497 (Rfree = 0.000) for 2333 atoms. Found 27 (151 requested) and removed 2 (80 requested) atoms. Cycle 49: After refmac, R = 0.2411 (Rfree = 0.000) for 2333 atoms. TimeTaking 96.28