Sun 23 Dec 22:22:43 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 1zbt-2.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zbt-2.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zbt-2.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-2.4-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/1zbt-2.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-2.4-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 22:22:51 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/1zbt-2.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-2.4-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 402 and 0 Target number of residues in the AU: 402 Target solvent content: 0.5493 Checking the provided sequence file Detected sequence length: 371 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 371 Adjusted target solvent content: 0.58 Input MTZ file: 1zbt-2.4-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: 71.823 71.823 187.134 90.000 90.000 90.000 Input sequence file: 1zbt-2.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2968 target number of atoms Had to go as low as 0.50 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 Loops will be built when appropriate and at the last cycle Resolution range: 28.608 2.403 Wilson plot Bfac: 35.29 19893 reflections ( 99.89 % complete ) and 0 restraints for refining 3267 atoms. Observations/parameters ratio is 1.52 ------------------------------------------------------ Starting model: R = 0.3344 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2731 (Rfree = 0.000) for 3267 atoms. Found 55 (66 requested) and removed 74 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.57 2.31 Round 1: 210 peptides, 26 chains. Longest chain 20 peptides. Score 0.544 Round 2: 230 peptides, 18 chains. Longest chain 51 peptides. Score 0.686 Round 3: 246 peptides, 15 chains. Longest chain 45 peptides. Score 0.746 Round 4: 250 peptides, 12 chains. Longest chain 48 peptides. Score 0.779 Round 5: 254 peptides, 14 chains. Longest chain 44 peptides. Score 0.768 Taking the results from Round 4 Chains 15, Residues 238, Estimated correctness of the model 92.0 % 7 chains (192 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 184 A and 187 A Built loop between residues 246 A and 253 A Built loop between residues 343 A and 346 A 11 chains (247 residues) following loop building 4 chains (202 residues) in sequence following loop building ------------------------------------------------------ 19893 reflections ( 99.89 % complete ) and 3388 restraints for refining 2796 atoms. 1625 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3003 (Rfree = 0.000) for 2796 atoms. Found 56 (56 requested) and removed 48 (28 requested) atoms. Cycle 2: After refmac, R = 0.2769 (Rfree = 0.000) for 2731 atoms. Found 52 (55 requested) and removed 42 (28 requested) atoms. Cycle 3: After refmac, R = 0.2554 (Rfree = 0.000) for 2711 atoms. Found 35 (53 requested) and removed 35 (27 requested) atoms. Cycle 4: After refmac, R = 0.2469 (Rfree = 0.000) for 2682 atoms. Found 26 (52 requested) and removed 35 (27 requested) atoms. Cycle 5: After refmac, R = 0.2362 (Rfree = 0.000) for 2659 atoms. Found 28 (50 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.50 2.25 Round 1: 245 peptides, 10 chains. Longest chain 73 peptides. Score 0.788 Round 2: 256 peptides, 7 chains. Longest chain 84 peptides. Score 0.827 Round 3: 259 peptides, 12 chains. Longest chain 54 peptides. Score 0.793 Round 4: 261 peptides, 9 chains. Longest chain 84 peptides. Score 0.819 Round 5: 258 peptides, 10 chains. Longest chain 63 peptides. Score 0.807 Taking the results from Round 2 Chains 7, Residues 249, Estimated correctness of the model 94.9 % 4 chains (213 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 242 A and 253 A 6 chains (259 residues) following loop building 3 chains (223 residues) in sequence following loop building ------------------------------------------------------ 19893 reflections ( 99.89 % complete ) and 3071 restraints for refining 2731 atoms. 1155 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2435 (Rfree = 0.000) for 2731 atoms. Found 31 (49 requested) and removed 34 (27 requested) atoms. Cycle 7: After refmac, R = 0.2271 (Rfree = 0.000) for 2715 atoms. Found 27 (48 requested) and removed 27 (27 requested) atoms. Cycle 8: After refmac, R = 0.2219 (Rfree = 0.000) for 2706 atoms. Found 26 (47 requested) and removed 28 (27 requested) atoms. Cycle 9: After refmac, R = 0.2157 (Rfree = 0.000) for 2696 atoms. Found 18 (45 requested) and removed 28 (27 requested) atoms. Cycle 10: After refmac, R = 0.2137 (Rfree = 0.000) for 2680 atoms. Found 33 (44 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.50 2.25 Round 1: 250 peptides, 10 chains. Longest chain 73 peptides. Score 0.795 Round 2: 252 peptides, 8 chains. Longest chain 63 peptides. Score 0.814 Round 3: 251 peptides, 12 chains. Longest chain 51 peptides. Score 0.780 Round 4: 255 peptides, 9 chains. Longest chain 72 peptides. Score 0.811 Round 5: 258 peptides, 14 chains. Longest chain 43 peptides. Score 0.775 Taking the results from Round 2 Chains 10, Residues 244, Estimated correctness of the model 94.1 % 5 chains (211 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 141 A and 148 A Built loop between residues 167 A and 170 A 8 chains (252 residues) following loop building 3 chains (219 residues) in sequence following loop building ------------------------------------------------------ 19893 reflections ( 99.89 % complete ) and 3126 restraints for refining 2702 atoms. 1241 conditional restraints added. Observations/parameters ratio is 1.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2230 (Rfree = 0.000) for 2702 atoms. Found 39 (44 requested) and removed 37 (27 requested) atoms. Cycle 12: After refmac, R = 0.2099 (Rfree = 0.000) for 2696 atoms. Found 25 (42 requested) and removed 28 (27 requested) atoms. Cycle 13: After refmac, R = 0.2049 (Rfree = 0.000) for 2688 atoms. Found 14 (41 requested) and removed 27 (27 requested) atoms. Cycle 14: After refmac, R = 0.2029 (Rfree = 0.000) for 2671 atoms. Found 11 (40 requested) and removed 27 (27 requested) atoms. Cycle 15: After refmac, R = 0.2008 (Rfree = 0.000) for 2654 atoms. Found 16 (38 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.49 2.24 Round 1: 252 peptides, 7 chains. Longest chain 79 peptides. Score 0.822 Round 2: 251 peptides, 10 chains. Longest chain 57 peptides. Score 0.797 Round 3: 257 peptides, 9 chains. Longest chain 68 peptides. Score 0.813 Round 4: 255 peptides, 10 chains. Longest chain 54 peptides. Score 0.803 Round 5: 257 peptides, 10 chains. Longest chain 62 peptides. Score 0.806 Taking the results from Round 1 Chains 9, Residues 245, Estimated correctness of the model 94.6 % 5 chains (221 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 144 A and 148 A Built loop between residues 162 A and 165 A Built loop between residues 242 A and 253 A 5 chains (259 residues) following loop building 2 chains (236 residues) in sequence following loop building ------------------------------------------------------ 19893 reflections ( 99.89 % complete ) and 2970 restraints for refining 2705 atoms. 998 conditional restraints added. Observations/parameters ratio is 1.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2219 (Rfree = 0.000) for 2705 atoms. Found 28 (38 requested) and removed 35 (27 requested) atoms. Cycle 17: After refmac, R = 0.2070 (Rfree = 0.000) for 2691 atoms. Found 19 (37 requested) and removed 27 (27 requested) atoms. Cycle 18: After refmac, R = 0.2008 (Rfree = 0.000) for 2676 atoms. Found 17 (36 requested) and removed 27 (27 requested) atoms. Cycle 19: After refmac, R = 0.1994 (Rfree = 0.000) for 2660 atoms. Found 19 (35 requested) and removed 28 (27 requested) atoms. Cycle 20: After refmac, R = 0.1975 (Rfree = 0.000) for 2651 atoms. Found 19 (33 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.49 2.24 Round 1: 255 peptides, 6 chains. Longest chain 73 peptides. Score 0.833 Round 2: 259 peptides, 8 chains. Longest chain 62 peptides. Score 0.824 Round 3: 256 peptides, 10 chains. Longest chain 60 peptides. Score 0.804 Round 4: 267 peptides, 7 chains. Longest chain 132 peptides. Score 0.841 Round 5: 261 peptides, 8 chains. Longest chain 126 peptides. Score 0.826 Taking the results from Round 4 Chains 9, Residues 260, Estimated correctness of the model 95.6 % 4 chains (213 residues) have been docked in sequence Building loops using Loopy2018 9 chains (260 residues) following loop building 4 chains (213 residues) in sequence following loop building ------------------------------------------------------ 19893 reflections ( 99.89 % complete ) and 3231 restraints for refining 2711 atoms. 1366 conditional restraints added. Observations/parameters ratio is 1.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2262 (Rfree = 0.000) for 2711 atoms. Found 33 (33 requested) and removed 34 (27 requested) atoms. Cycle 22: After refmac, R = 0.2085 (Rfree = 0.000) for 2702 atoms. Found 17 (31 requested) and removed 28 (27 requested) atoms. Cycle 23: After refmac, R = 0.2012 (Rfree = 0.000) for 2688 atoms. Found 16 (30 requested) and removed 28 (27 requested) atoms. Cycle 24: After refmac, R = 0.1985 (Rfree = 0.000) for 2676 atoms. Found 18 (29 requested) and removed 27 (27 requested) atoms. Cycle 25: After refmac, R = 0.1990 (Rfree = 0.000) for 2662 atoms. Found 26 (28 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.49 2.24 Round 1: 263 peptides, 7 chains. Longest chain 71 peptides. Score 0.836 Round 2: 259 peptides, 7 chains. Longest chain 73 peptides. Score 0.831 Round 3: 260 peptides, 9 chains. Longest chain 85 peptides. Score 0.817 Round 4: 257 peptides, 10 chains. Longest chain 61 peptides. Score 0.806 Round 5: 260 peptides, 8 chains. Longest chain 90 peptides. Score 0.825 Taking the results from Round 1 Chains 8, Residues 256, Estimated correctness of the model 95.3 % 5 chains (234 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 169 A and 173 A Built loop between residues 241 A and 252 A Built loop between residues 270 A and 273 A 4 chains (270 residues) following loop building 2 chains (249 residues) in sequence following loop building ------------------------------------------------------ 19893 reflections ( 99.89 % complete ) and 2994 restraints for refining 2797 atoms. 902 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2358 (Rfree = 0.000) for 2797 atoms. Found 28 (28 requested) and removed 46 (28 requested) atoms. Cycle 27: After refmac, R = 0.2128 (Rfree = 0.000) for 2769 atoms. Found 28 (28 requested) and removed 28 (28 requested) atoms. Cycle 28: After refmac, R = 0.2022 (Rfree = 0.000) for 2765 atoms. Found 19 (28 requested) and removed 30 (28 requested) atoms. Cycle 29: After refmac, R = 0.1969 (Rfree = 0.000) for 2750 atoms. Found 21 (27 requested) and removed 28 (27 requested) atoms. Cycle 30: After refmac, R = 0.1966 (Rfree = 0.000) for 2738 atoms. Found 19 (27 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.48 2.23 Round 1: 266 peptides, 6 chains. Longest chain 71 peptides. Score 0.847 Round 2: 261 peptides, 9 chains. Longest chain 72 peptides. Score 0.819 Round 3: 254 peptides, 11 chains. Longest chain 54 peptides. Score 0.793 Round 4: 255 peptides, 9 chains. Longest chain 54 peptides. Score 0.811 Round 5: 260 peptides, 10 chains. Longest chain 55 peptides. Score 0.810 Taking the results from Round 1 Chains 6, Residues 260, Estimated correctness of the model 95.9 % 4 chains (239 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 169 A and 173 A Built loop between residues 242 A and 253 A 4 chains (273 residues) following loop building 2 chains (252 residues) in sequence following loop building ------------------------------------------------------ 19893 reflections ( 99.89 % complete ) and 2931 restraints for refining 2797 atoms. 812 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2339 (Rfree = 0.000) for 2797 atoms. Found 28 (28 requested) and removed 46 (28 requested) atoms. Cycle 32: After refmac, R = 0.2116 (Rfree = 0.000) for 2771 atoms. Found 28 (28 requested) and removed 31 (28 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2035 (Rfree = 0.000) for 2765 atoms. Found 21 (28 requested) and removed 31 (28 requested) atoms. Cycle 34: After refmac, R = 0.1979 (Rfree = 0.000) for 2750 atoms. Found 21 (27 requested) and removed 28 (27 requested) atoms. Cycle 35: After refmac, R = 0.1969 (Rfree = 0.000) for 2739 atoms. Found 17 (27 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.49 2.24 Round 1: 260 peptides, 8 chains. Longest chain 72 peptides. Score 0.825 Round 2: 256 peptides, 10 chains. Longest chain 73 peptides. Score 0.804 Round 3: 260 peptides, 10 chains. Longest chain 61 peptides. Score 0.810 Round 4: 253 peptides, 11 chains. Longest chain 54 peptides. Score 0.792 Round 5: 253 peptides, 9 chains. Longest chain 59 peptides. Score 0.808 Taking the results from Round 1 Chains 8, Residues 252, Estimated correctness of the model 94.8 % 4 chains (225 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 163 A and 173 A Built loop between residues 243 A and 252 A 5 chains (266 residues) following loop building 2 chains (242 residues) in sequence following loop building ------------------------------------------------------ 19893 reflections ( 99.89 % complete ) and 3053 restraints for refining 2797 atoms. 1026 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2329 (Rfree = 0.000) for 2797 atoms. Found 28 (28 requested) and removed 45 (28 requested) atoms. Cycle 37: After refmac, R = 0.2139 (Rfree = 0.000) for 2770 atoms. Found 28 (28 requested) and removed 29 (28 requested) atoms. Cycle 38: After refmac, R = 0.2034 (Rfree = 0.000) for 2766 atoms. Found 21 (28 requested) and removed 28 (28 requested) atoms. Cycle 39: After refmac, R = 0.1960 (Rfree = 0.000) for 2755 atoms. Found 11 (27 requested) and removed 30 (27 requested) atoms. Cycle 40: After refmac, R = 0.1957 (Rfree = 0.000) for 2734 atoms. Found 18 (27 requested) and removed 29 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.50 2.25 Round 1: 252 peptides, 7 chains. Longest chain 132 peptides. Score 0.822 Round 2: 257 peptides, 5 chains. Longest chain 133 peptides. Score 0.843 Round 3: 254 peptides, 8 chains. Longest chain 57 peptides. Score 0.817 Round 4: 260 peptides, 8 chains. Longest chain 119 peptides. Score 0.825 Round 5: 258 peptides, 8 chains. Longest chain 83 peptides. Score 0.822 Taking the results from Round 2 Chains 5, Residues 252, Estimated correctness of the model 95.7 % 3 chains (232 residues) have been docked in sequence Building loops using Loopy2018 5 chains (252 residues) following loop building 3 chains (232 residues) in sequence following loop building ------------------------------------------------------ 19893 reflections ( 99.89 % complete ) and 3098 restraints for refining 2792 atoms. 1147 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2246 (Rfree = 0.000) for 2792 atoms. Found 28 (28 requested) and removed 45 (28 requested) atoms. Cycle 42: After refmac, R = 0.2043 (Rfree = 0.000) for 2770 atoms. Found 20 (28 requested) and removed 30 (28 requested) atoms. Cycle 43: After refmac, R = 0.1983 (Rfree = 0.000) for 2758 atoms. Found 19 (28 requested) and removed 30 (28 requested) atoms. Cycle 44: After refmac, R = 0.1958 (Rfree = 0.000) for 2742 atoms. Found 21 (27 requested) and removed 28 (27 requested) atoms. Cycle 45: After refmac, R = 0.1948 (Rfree = 0.000) for 2730 atoms. Found 27 (27 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.50 2.25 Round 1: 254 peptides, 6 chains. Longest chain 72 peptides. Score 0.832 Round 2: 253 peptides, 7 chains. Longest chain 70 peptides. Score 0.823 Round 3: 253 peptides, 10 chains. Longest chain 72 peptides. Score 0.800 Round 4: 254 peptides, 9 chains. Longest chain 60 peptides. Score 0.809 Round 5: 251 peptides, 7 chains. Longest chain 61 peptides. Score 0.821 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 248, Estimated correctness of the model 95.1 % 4 chains (227 residues) have been docked in sequence Sequence coverage is 91 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 169 A and 173 A 6 chains (251 residues) following loop building 3 chains (230 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 19893 reflections ( 99.89 % complete ) and 1933 restraints for refining 1911 atoms. Observations/parameters ratio is 2.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3069 (Rfree = 0.000) for 1911 atoms. Found 19 (19 requested) and removed 0 (19 requested) atoms. Cycle 47: After refmac, R = 0.2895 (Rfree = 0.000) for 1911 atoms. Found 10 (19 requested) and removed 0 (19 requested) atoms. Cycle 48: After refmac, R = 0.2829 (Rfree = 0.000) for 1911 atoms. Found 6 (19 requested) and removed 0 (19 requested) atoms. Cycle 49: After refmac, R = 0.2808 (Rfree = 0.000) for 1911 atoms. TimeTaking 57.7